Haplogroup Matching: What It Does (and Doesn’t) Mean

“Our haplogroups (sort of) match, so that means we’re related, right?”

Well, maybe.

It depends.

Great Question

This is an oft-asked great question. Of course, the answer varies depending on the context of the question and what is meant by “related.” A haplogroup match may or may not be a valid match for genealogy. A “match” or a “not match” can mean different things.

The questions people often ask include:

  • Does a haplogroup have to match exactly in order for another person to either be considered a match to you?
  • If they don’t match exactly, can they still be considered as a possible match?
  • Conversely, can we rule someone out as a match on a specific genealogical line based on haplogroup alone?

These questions often arise in relation to DNA testing at Family Tree DNA, sometimes when people are trying to compare results to people who have haplogroup estimates, either at FamilyTreeDNA or from testing elsewhere.

In other words, if one person is haplogroup J and someone else is J1, either at the same vendor or at another, what does that tell us? This question pertains to both Y DNA and mitochondrial DNA tests no matter where you’ve tested.

Family Tree DNA offers different levels of Y DNA testing. Interpreting those match results can sometimes be confusing. The same is true for mitochondrial DNA, especially if your matches have not taken the full mitochondrial sequence (mtFull) test.

You might be comparing apples and oranges, or you might be comparing a whole orange (detailed test) with a few slices (haplogroup estimate.) How can you know, and how can you make sense of the results?

If you’re comparing a haplogroup between sources, such as a partial haplogroup determined by testing through a company like 23andMe or LivingDNA to complete tests taken at FamilyTreeDNA, the answer can be less than straightforward.

I discussed the difference between autosomal-based haplogroup assignments and actual testing of both Y DNA and mitochondrial DNA which result in haplogroup assignments, here. In a nutshell, both LivingDNA and 23andMe provide a high-level (base) haplogroup estimates based on a few specific probes when you purchase an autosomal test, but that’s not the same as deeper testing of the Y chromosome or mitochondrial DNA.

The answer to whether your haplogroup has to match is both “yes”, and “no.” Don’t you hate it when this happens?

Let’s look at different situations. But to begin with, there is at least one common answer.

Yes, Your Base Haplogroup Must Match

To even begin to look further for a common ancestor on either your Y DNA line (direct patrilineal) or direct mitochondrial matrilineal line (your mother’s mother’s mother’s line on up the tree), your base haplogroup much match.

In other words, you and your matches must all be in the same base haplogroup. Haplogroups are defined by the presence of specific combinations of mutations which are called SNPs (single nucleotide polymorphisms) in the Y DNA.

Click to enlarge images

All of these men on the Y DNA matches page are a branch of haplogroup R as shown under the Y-DNA Haplogroup column. There are more matches on down the page (not shown here) with more and different haplogroups. However, you’ll notice that all matches are a subset of haplogroup R, the base haplogroup.

The same is true for mitochondrial DNA haplogroups. You can see in this example that people who have not tested at the FMS (full mitochondrial sequence) level have a less specific haplogroup. The entire mitochondria must be tested in order to obtain a full haplogroup, such as J1c2f, as opposed to haplogroup J.

The Y DNA Terminal SNP Might Not Match

For Y DNA testers, when looking at your matches, even to close relatives, you may not have the same exact haplogroup because:

  • Some people may have tested at different levels
  • Some people in recent generations may have developed a SNP specific to their line.

In other words, haplogroups, testing level, and known genealogy all need to be considered, especially when the haplogroups are “close to each other” on the tree.

For Y DNA, FamilyTreeDNA:

  • Provides all testers with base haplogroup estimates based on STR tests, meaning 12-111 marker panels. These are very accurate estimates, but are also very high level.
  • Offers or has offered in the past both individual SNP tests and SNP packs or bundles that test individual SNPs indicating their presence or absence. This confirms a SNP or haplogroup, but only to that particular level.
  • Offers the Big Y-700 test, along with upgrades to previous Big Y test levels. There have been 3 versions of the Big Y test over time. The Big Y reads the entire gold standard region of the Y chromosome, reporting the known (named) SNP mutations customers do and don’t have. Additionally, the test reports any unnamed SNPs which are considered private variants until multiple men on the same branch of the Y DNA tree test with the same mutation. At that point, the mutation is named and becomes a haplogroup.

That’s why the answer is “no,” your haplogroup does not have to match exactly for you to actually be a match to each other.

A father and son could test, with one having an estimated haplogroup of R-M269 and the other taking the Big Y-700 resulting in a very different Terminal SNP, quite distant on the tree. Conversely, both men could take the Big Y and the son could have a different terminal SNP than the father because a mutation occurred between them. An autosomal DNA test would confirm that they are in fact, father and son.

However, a father and son who test and are placed in different base haplogroups – one in haplogroup I, and the other in haplogroup R, for example, has a very different situation. Their autosomal test would likely confirm that they are not father and son.

Having said this about paternity, especially if haplogroups are estimated and specific Y DNA SNP testing has not been done, don’t have a premature freak-out moment. Look at autosomal DNA, assuming you DO want to know. Y DNA alone should never be used to infer paternity without autosomal testing.

Let’s look at some examples.

Matches and Haplogroups

In the example shown above, you can see that several people have taken the Big Y test, so their SNP will be shown on further down the haplotree than those testers who have not. These are a leaf, not a branch.

You can see by looking at the Terminal SNP column, at far right, that people who have either taken the Big Y, or had any positive SNP test will have a value in the Terminal SNP column.

Anyone who has NOT taken the Big Y or taken a SNP test will have their base haplogroup estimated based on their STR tests. In this case, that estimate is R-M269. People with estimated haplogroups will not show anything in the Terminal SNP column.

It’s possible that if all of these men took the Big Y test that at least some would share the same Terminal SNP, and others might be closely related, only a branch or so different on the tree.

These men in this example are all descendants of Robert Estes born in England in 1555. All have Estes surnames, except for one man who is seeking the identity of his paternal line.

Let’s Look at the Tree

Our tester in the screenshot is haplogroup R-ZS3700 and matches men in the following haplogroups:

  • R-M269
  • R-L21
  • R-BY490
  • R-BY154784

There are a few additional haplogroups not shown because they are further down on his match list, so let’s just work with these for now.

After determining that these men are on the same branch of the Y tree, haplogroup R, the real question is how closely they are related and how close or far distant their terminal SNPs are located. More distance means the common ancestor is further back in time.

However, looks can be deceiving, especially if not everyone has tested to the same level.

The haplogroup furthest up in the tree, meaning the oldest, is R-M269, followed by the man who took the single SNP test for R-L21. Notice that R-M269 has more than 15,000 branches, so while this haplogroup could be used to rule out a match, R-M269 alone isn’t useful to determine genealogical matching.

There are a lot of branches between R-L21 and the next haplogroup on the tree.

Finally, here we go. Our tester is haplogroup R-ZS3700 that has one descendant branch. R-ZS3700 is a branch of R-BY490 that has 2 branches.

R-BY154784 is the last SNP on this branch of the tree. Our tester matches this man too.

Another way of viewing these matches is on the Block Tree provided for Big Y testers.

In this view, you can see that the Estes men all match back to about 18 “SNP generations” ago according to the legend at left, but they don’t match men further back in time who have taken the Big Y test.

Notice the up-arrow where haplogroups R-L21 and R-M269 are shown across the top of the display.

If you click on R-L21, you’ll see that that it appears about 61 SNP generations back in time.

Haplogroup R-M269 appears even further back in time, about 174 SNP generations.

The only reason you will match someone at either the R-L21 or R-M269 level is because you both descend from a common long-ago ancestral branch, hundreds to thousands of years in the past. You and they would both need to take either the Big Y-700 test for Y DNA, or the full sequence mitochondrial DNA test in order to determine your full haplogroup and see your list of matches based on those full sequences.

Public Trees

You can view FamilyTreeDNA‘s extensive public Y DNA tree by haplogroup, here.

You can view their public mitochondrial DNA tree by haplogroup, here.

And the Answer Is…

As you can see, there is no single answer to the question of haplogroup relationships. The answer is also partly defined by the context in which the question is asked.

  1. For two men to be “related” on the Y DNA patrilineal line, yes, minimally, the base haplogroup does have to match. Base haplogroups are defined by the leading letter, like “R” in the examples above.
  2. “Related” based on base haplogroup only can be hundreds or thousands of years back in time, but additional testing can resolve that question.
  3. “Related” can mean before the advent of surnames. However, a match to a man with the same surname suggests a common ancestor with that surname in the past several hundred years. That match could, however, be much closer in time.
  4. For two men to be closely related, assuming they have taken the same version of Big Y test, their haplogroup branches need to be fairly closely adjacent on the haplotree. FamilyTreeDNA will be introducing haplogroup aging soon, meaning SNP/haplogroup branch dates on their haplotree. At that time, the “distance” between men will be easier to understand.
  5. You can exclude a genealogical relationship on the direct paternal line if the two men involved have a different base haplogroup. This question often occurs when people are trying to understand if they “might match” with someone whose haplogroup has been estimated.
  6. This holds true as well for mitochondrial DNA haplogroups and matching.

And there you have it, six answers about what haplogroup matching does and does not mean.

The bottom line is that haplogroups can be a great starting point and you can sometimes eliminate people as potential matches.

However, to confirm genealogical matches, you’ll always need more granular testing that includes actual Y DNA or mitochondrial DNA matching based on marker mutation results, not just haplogroups.



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41 thoughts on “Haplogroup Matching: What It Does (and Doesn’t) Mean

  1. My real concerns with current FTDNA Haplogroup BigY-700 tests and terminal SNP issues relates to what happens when you have concerns over branching SNP details in the time period 1650-1800. The only way you seem to be able to get at discrepancies which emerge there between documentation hypotheses and BigY-700 testing is to call for a personal thorough review of all tested folk in that date range to see if there are any genuine new branch marking Y-SNPs that can be gleaned. That is the situation I have right now with one of my major Swan(n) lines from Maryland – and it is somewhat frustrating.

  2. After much expansion of my tree, I found a 3C on 23andMe who, according to the paper trail is in a matrilineal line of descent from my matrilineal 3rd great grandmother from County Mayo, Ireland. Her mtDNA haplogroup is J1c1. My haplogroup is J1c1b1. This seems reasonable to me since this is not a full sequence test, so it is a small bit of support in building evidence for my tree. Hopefully, budgets will permit full sequence testing at some point.

    My question is, given that this is more of an estimate, is it equally likely that my actual haplogroup would be J1c1 as it is that hers would be J1c1b1? Can this estimate work either way? Is it possible we could both be just J1c? Or is it more likely we are J1cib1 or downstream of that?

  3. Your Estes Y-DNA is very close to my son’s, with the same problems. He increased his Family Tree Y-DNA to 111 markers which proved his R-Z326 haplogroup. He needs to upgrade to one of the Big Y tests, but I saw no use in doing this until he had close matches. He now has close matches.

    What people should know is that every time there is an increase in the markers tested, some of the closest matches are no longer that close. A zero distance match is now a three, but a previous two distance match remains a two.

    I am not sure what a two distance means in years? Is autosomal matches possible? What I have here is a two distance match between Taylor and Tyler.

  4. I love the block tree.
    FTDNA is great for taking it up for YDNA.
    I would love it if they also adopted it for mtDNA.
    Even if it were only in mtDNA Haplogroup Projects.
    At present we are where YDNA was about a decade ago.
    A block tree would really help people understand mtDNA.
    And maybe encourage more people to test – so we could see a bit more structure.

    After talking to some of my close matches I know there are some rough regional groupings that should be possible, and this would help us with that.

    You are just about the only person I can think of blogging about mtDNA being useful.
    Maybe there can be a push before this year’s mothers day?

    • That’s a good idea about an mtDNA block tree. Both Judy Russell and Elizabeth Shown Mills have written about mtDNA too. Judy just a few days ago again.

  5. I had cold sweat last year when I tested my maternal uncle. I knew there were at least two distant cousins, as I saw them in a project database. When the Y37 results came back, I had no match among the 26-37… no match among the 13-25… searching through the Y12 with the search box, I finally found them. I knew from a previous email exchange with the project admins that they where from a different son of the pionner ancestor, but only Y12, were we cousins before early Bronze age?

    Long story short, I joined the same project and contacted the admins for their assessment. My uncle has a “bump” of 4 mutations at the 13-25 area, but the rest of the mutations fit for 8th cousins. We all tested further now, and my uncle match them back at Y67 and Y111. Plus Big Y makes it obvious no other men in the daabase is as close as these three men between each other.

    That was a long week, as you can imagine.

      • Not so much for myself, with DNA, I always brace for the worst possible outcome waiting for results and live by “what is, is”, but how to explain it to my uncle who knew results would come.

        But once it was clear everything was legit, how to explain it to distant cousins? “Hello, we may only be Y-12 matches, but we are close cousins, believe me!” and “we will become close match if you only agree to spend even more money that you ever did on this and test deeper, believe me!”.

        Thank you ever so much for these Y-DNA articles, I manage to convince both to pay for Big Y. ^__^

  6. Not rocket science. Haplogroups are trees that have labels for each decrease in common ancestor back to the earliest. Example (let’s take ‘J’ since there’s one for Y and one for mt):
    Haplogroup J is your earliest direct line ancestor. J1 is the next earliest, and so on.
    J1 J2

  7. Hello Friends!

    Thought I’d share my yDNA testing experience at FTDNA. I first tested at 37 markers before upgrading to 67.

    Some basic stats:
    Haplogrou = r-m269
    Y12 – 16,978 matches,
    Y25 – 2,118 matches
    Y37 – 53 matches
    Y67 – 35 matches

    The y37 and y67 matches are clustered around a specific group of men who trace to multiple immigrations mostly from England and a few from Southern Scotland to the east coast of the US.

    I have not tested at y111 or tested the specific SNPs unique to group of men I match. My 3C1R cousin tested and matches me, so we confirmed our 2G grandfathers had the same father, whom we believe is the 3G grandfather we’ve always known about.

    Interestingly, I do not match a single one of my ydna matches from the y37 or y67 test in an autosomal dna test.

    If I test at y111 or get the specific SNP tests (or a SNP bulk pack) should I be able to confirm when my ydna haplogroup split off the main branch? Or if there has been an unlikely case of convergence?

    How likely would it also confirm if any most distant known male ancestors of my ydna brothers are potential grandfathers for me or not? Many people descending from that family have done autosomal dna tests and don’t match me or my 60+ cousins.

    Question about Convergence: how often does that really happen within a ydna haplogroup? How often do ydna STR changes occur so that they match a STR and triggers a haplogroup match?

    Gee….i really need to upgrade my SNP tests. Don’t I?

    What if I don’t see the SNP at ftdna on which my ydna cousins tested?

    Is everything tested in y700 or Big y available as individual SNP or bulk SNP tests?

  8. Now I have a question about FTDNA. I’m looking at the haplogroup tree and all the SNPs listed. My ydna test ‘presumed positive’. I’m looking at the little downstream blue dots. That means i haven’t tested positive for those variants, but a test would verify or not i i had that variant? Thereby placing me more accurately somewhere in the haplogroup?

  9. I did Big Y 700 and two other people with the same surname match. One has a distance of 7 and the other a distance of 8. I think our most recent common ancestor we share may have lived in the 1600s in Scotland. The weird thing is my 4th great-grandfather’s census says he’s from Germany. I think maybe one of the sons had migrated to Germany from Scotland and then either him or one of his sons came to America. Have you heard of anything such as this type of migration happening? The surnames in my match list appear to be mostly Scottish too. Isn’t that an indication that my ancestor was most likely Scottish? My haplogroup is R1B-L1335 or 1065.

  10. It’s really hard to find information from the 1600s UK. From what I read you have to go there to the parish you think your ancestor came from and review the records in person. I was wondering if there are other Y DNA databases in the UK that I could check to see if I have any matches with? That would be nice if you could send your FTDNA Y-DNA to another company in the UK and check.

  11. Thank you for this article. In your Block Tree image, you state that the Estes men don’t match other testers back further than 19 SNP generations. But of course they are related since they are all descended from R-FT1796. I suggest that the article needs the FTDNA definition of what a “Match” is.

    Also, you state, “However, to confirm genealogical matches, you’ll always need more granular testing that includes actual Y DNA or mitochondrial DNA matching based on marker mutation results, not just haplogroups.” Why do you say that? I just tested a 7th cousin with Y-700 and we both have the same terminal haplogroup — that genealogical match is confirmed.

  12. Thank you for this article. In your Block Tree image, you state that the Estes men don’t match other testers back further than 19 SNP generations. But of course they are related since they are all descended from R-FT1796. May I suggest that you add an FTDNA definition of what a “Match” is.

    Also, you state, “However, to confirm genealogical matches, you’ll always need more granular testing that includes actual Y DNA or mitochondrial DNA matching based on marker mutation results, not just haplogroups.” Why do you say that? I just tested a 7th cousin with Y-700 and we both have the same terminal haplogroup — that genealogical match is confirmed.

    • That comment is about having a “haplogroup only” match at the higher estimated level. Like R-M269 for example or at one of the companies that does not do Y or mtDNA testing. Many people match just at the haplogroup level. Having said that, a Big Y-700 will confirm a very granular haplogroup, but it still doesn’t confirm the genealogical relationship of which male in that line was the paternal ancestor.

  13. This is so helpful! I have a question about MTDNA base haplogroups regarding searching for my birth mother. I am a male and my MTDNA Haplogroup is A2 (FTDNA) and I have a good match (S.S.) who is Haplogroup L3B. (Additionally I match this person on the X and I understand that I can only inherit the X maternally but a female (S.S.) can inherit this from either parent.) So if I understand regarding MTDNA haplogroups because I do not match the base MTDNA haplogroup as S.S. (but also match her on the X) then I match S.S. through her paternal line?

  14. Thank you for writing this ‘somewhat’ clear explanation for those of us who are struggling with the technical side of DNA.

    I am trying to pull together some straggler lines in my tree and I have tested at 23andMe, Ancestry, FTDNA and MyHeritage. I am a female, but I have strong autosomal matches with several male cousins who supposedly all descend from my g-grandfather. In my tree, there are also several children were who given up for adoption so trying to figure out who fathered/mothered any of them has been a TRUE challenge.

    I hope you can help me to understand this further as it applies to my tree. For the sake of simplicity, I’ve pared down the generations:
    My g-grandfather (born 1849) had 3 sons. Each son had a son, who had a son, who had a son. (My grandfather (born 1875) also had a daughter and that’s my lineage).

    I have matches with all three in autosomal testing, but when I compare their results in 23andMe, 2 of the sons have R-S660 Haplogroup and one has E-M4451 (clearly I don’t have a y-DNA Haplogroup).

    Would these results indicate that the one who has the E-M4451 Haplogroup is the one with a father that is NOT of the same lineage? I mean…it would be impossible for a direct male descendant to change Haplogroups to this extreme…right?


  15. Thank you! Now I know which child was mothered and not fathered from the lineage. Believe it or not, his helps immensely!

  16. Hello, what about when 2 different Haplogroups have the same mutation in the same time/ stream? Does it mean there was some relation at that time i.e. 2 half brothers with different dad’s? e.g. E-Y64337 & J1-Y64337 genetic variation rs765193478.

  17. What does it mean when mom is H7a1 and daughter is H7a and granddaughter is H7a are they still considered a match?

    • If they are that closely related, yes. Part of the mismatch could be based on testing at different companies, or a mutation.

  18. I’m a bit late to this post sorry, but it’s helpful in trying to interpret my father’s Big Y results. With regard to the Y haplo tree will all men who funnel through a part of that (eg R-M269) all be on the same path prior to that point? Or are there many paths that go via R-M269?
    You say “The only reason you will match someone at either the R-L21 or R-M269 level is because you both descend from a common long-ago ancestral branch” so I was just trying to clarify that.

    Thanks so much 🙂

      • Great, that’s helpful thanks. Actually my father has no matches in the Big Y 700 but there are some distant men in the Y- dna tab.
        Another question about the haplo – after the common point (eg R-M269) I know there are many paths down to various terminal points.
        On my father’s path he has some (12 marker only) matches at some points along the way. At R-M269 he has 3222 matches (approx half his total Y matches), next at L23 he has 1 match, next at L51 he has 3, none at the next position ….. etc at U152 he has 13 matches ….
        Is this the usual pattern?
        And not all U152 men will match him or be on his same path?

        • What I think I hear you saying is that only a few men have L51, for example. This is a function of only a few men having tested that terminal SNP. Now, with the Big Y – there will be more men with more refined haplogroups that probably do have L51 further up their tree.

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