X Matching and Mitochondrial DNA is Not the Same Thing

Recently, I’ve noticed a lot of confusion surrounding X DNA matching and mitochondrial DNA. Some folks think they are the same thing, but they aren’t at all.

It’s easy to become confused by the different types of DNA that we can use for genealogy, so I’ll try to explain these differences two or three different ways – and hopefully one of them will be just the ticket for you.

Both Associated with Females

I suspect the confusion has to do with the fact that mitochondrial DNA and the X chromosome are both associated in some manner with female inheritance. However, that isn’t always true in the strictest sense, as women also inherit an X chromosome from their father.

Males Inherit:

  • An X chromosome from their mother
  • Mitochondrial DNA from their mother

Females Inherit:

  • An X chromosome from their mother
  • An X chromosome from their father
  • Mitochondrial DNA from their mother

The difference, as you can quickly see, is that females inherit an X chromosome from both parents, while males only inherit the X from their mothers. That’s because males inherit the Y chromosome from their father instead – which is what makes males male.

As a quick overview about inheritance works, you might want to read the article, 4 Kinds of DNA for Genetic Genealogy.

The good news is that both mitochondrial DNA and the X chromosome have very specific inheritance paths that can be very useful to genealogy, once you understand how they work.

Who Gets What?

Mitochondrial DNA Inheritance

Mitochondrial DNA is inherited by both genders of children from their mothers. Mitochondrial DNA is NEVER recombined with the mitochondrial DNA of the father – so it’s passed intact. That’s why both males and females can test for their direct matrilineal line through their mitochondrial DNA.

In the pedigree chart above, you can see that mtDNA (red circles) is passed directly down the matrilineal line, while Y DNA is passed directly down the patrilineal (surname) line (blue squares.)

I’ve written an in-depth article titled, Mitochondrial DNA – Your Mom’s Story that might be useful to read, as well as Working with Y DNA – Your Dad’s Story.

The X Chromosome

The X Chromosome is autosomal, meaning that it recombines in every generation. If you are a female, the X recombines just like any other autosome, meaning chromosomes 1-22. You receive a copy from each parent.

The 23rd pair of chromosomes is the X and Y chromosomes which convey gender. Males receive an X from their mother and Y from their father. The Y chromosome makes males male. Females receive an X chromosome from both parents, just like the rest of chromosomes 1-22.

Inheritance Pathways

If you are a male, the inheritance path of the X chromosome is a bit different from that of a female, because you inherit your X only from your mother.

Females inherit their father’s ONLY X chromosome intact, which he inherited from his mother. Females inherit their X chromosome from their mother in the normal autosomal way. A mother has two X chromosomes, so the mother can give a child either chromosome entirely or parts of both of her X chromosomes.

Because of the different ways that males and females inherit the X chromosome, the inheritance path is different than chromosomes 1-22, portions of which you can inherit from any of your ancestors. Conversely, you can only inherit portions of your X chromosome from certain ancestors. You can read about more about this in the article, X Marks the Spot.

Female X inheritance chart. For male distribution, look at my father’s side of the tree.

My own colorized X chromosome chart is shown above, produced from my genealogy software and Charting Companion. An X match MUST COME from one of the ancestors in the pink and blue colored quadrants. It’s very unlikely that I would inherit parts of my X chromosome from all of these ancestors, but these ancestors are the only candidates from whom my X originated. In other words, genealogically, these are the only ancestors for me to investigate when I have an X DNA match with someone.

Because of this unbalanced distribution of the X chromosome, if you are a male and you match someone on the X chromosome, assuming it’s a legitimate match and not a match by chance, then you know the match MUST come from your mother’s side of the family, and only from her pink and blue colored ancestors – looking at my father’s half of the tree as an example.

If you are a female the match can come from either side, but only from a restricted number of individuals – those colored pink or blue, as shown above.

X chart with Y line included in purple, for males, and mitochondrial line in green.

My mitochondrial line, shown on the X chart would consist of only the women on the bottom row, extending to the right from me, colored in green above. My father’s Y DNA line would be the purple region, extending along the bottom at left. Of course, I don’t have a Y chromosome, because I’m female.

Of the individuals carrying the purple Y DNA, the only one with an X chromosome that a female could inherit would be the father. A female would inherit both the mtDNA of all of the green women, plus could also inherit an X chromosome (or part of an X) from them too.

For males, looking at my father’s half of the chart. He can inherit no X chromosome from any of the purple Y DNA portion, because those men gave him their Y chromosome. My father would inherit his mitochondrial DNA from his direct matrilineal line, shown in yellow, below.

X chart with mitochondrial inheritance line for mother (and child) shown in green, for father shown in yellow.  Both yellow and green lines can contribute to the X chromosome for males and females.

In my father’s case, the females in his tree that he can inherit an X chromosome from are quite limited, but people who have the opportunity to pass their X chromosome to my father are never restricted to only the people that pass his mitochondrial DNA to him. However, the X chromosome contributors always include the mitochondrial DNA contributors for both males and females.

In my father’s case, above, he inherits his X chromosome from his mother, who can only inherit her X from the people on his side of the chart shown in yellow, blue or pink. In essence, the people in yellow or to the left of the yellow with any color.

As his daughter, I can inherit from any of those ancestors as well, since he gives me his only X, who he inherited from his mother. I also inherit an X from my mother from anyone who is green, pink or blue on her side of my chart.

As you can see, my X can come from many fewer ancestors on my father’s side than on my mother’s side.

It just happens that ancestors in the mitochondrial line also are able to contribute an X chromosome and either gender can inherit parts of their X chromosome from any female upstream of their mother in the direct matrilineal line. However, only the direct matrilineal line (yellow for your father and green for your mother) contributes mitochondrial DNA. None of the other ancestors contribute mtDNA to this male or female, although females contribute their mtDNA to other individuals in the tree. For a more detailed discussion on inheritance, please read the article, “Concepts – ‘Who to Test Series”.

Special Treatment for X Matches

While the generally accepted threshold for autosomal DNA is about 7cM, for X DNA, there appears to be a much higher incidence of false matches at higher levels than the rest of the chromosomes, as documented by Philip Gammon as in his Match-Maker-Breaker tool.  This appears to have to do with SNP density.

I would encourage genetic genealogists to consider someplace between 10 and 15 cM as an acceptable threshold for an X chromosome match. This of course does not mean that smaller segment matching can’t be relevant, it’s just that X matches are less likely to be relevant at levels below 10-15 cM than the rest of the chromosomes.


As you can see, the mitochondrial DNA is passed from one line only – the direct matrilineal line – green to my mother and then me, yellow to my father. The mitochondrial DNA has absolutely NOTHING to do with the X chromosome, as they are entirely different kinds of DNA. It just so happens that the individuals who contribute mitochondrial DNA are also some of the ancestors who can contribute an X chromosome to either males or females.

The yellow and green ancestors always contribute mitochondrial DNA, but the pink and blue NEVER contribute mitochondrial DNA to the father and mother in our chart.

The X chromosome has a very distinctive inheritance path, shown in the first fan chart, that will help identify potential ancestors who may have contributed your X chromosome – which is wonderful for genealogists. If your ancestor is not colored pink or blue, in the first chart, they did not contribute anything to your X chromosome – so an X match MUST come from a pink or blue ancestor (which includes yellow and green in the later charts.)

By color, the people in the fan chart provide the following:

  • Purple – Y chromosome to father only.  Y is passed on to a male child, but not to females.
  • Yellow – Mitochondrial always to father. X always from mother to males but X can come from either yellow or pink and blue ancestors upstream.
  • Green – Mitochondrial always to the mother.  Females receive an X chromosome from their green mother and also from their father, who received his X chromosome from his yellow mother.
  • PInk and blue on father’s side – contribute to the father’s X chromosome, in addition to yellow.
  • Pink and blue on mother’s side – contribute to the mother’s X chromosome, in addition to green.


If you are a male and see an X match on your father’s side of the tree, you know that match is either actually coming from your mother’s side of the tree, or the match is false, meaning identical by chance.

The great news is that X matching is another tool with special attributes in the genealogist’s toolbox, along with both mitochondrial and Y DNA.

Your X chromosome test is included as part of the Family Finder test. You can order the Family Finder or the mitochondrial DNA tests here.



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65 thoughts on “X Matching and Mitochondrial DNA is Not the Same Thing

  1. Very informative and easy to understand. I have Moores, Campbells, and ,Munsey/Muncys in my tree also.

  2. My five siblings and I inherited both our mtDNA and an X chromosome from our mother, but for two of us that’s as far as the two types of DNA travel the same path.

    My brother Bernie and my sister Kim both inherited an X chromosome that is entirely traceable to our maternal *grandfather*. The mtDNA path, of course, goes through our maternal grandmother.

    Unlike the two siblings I named, I inherited part of my X chromosome from my grandmother — but only 20 cM surrounding the centromere. There are some folks who match me here, which has also made it possible to determine this portion of my X chromosome is also attributable to my grandmother’s mother, and my grandmother’s grandmother. Beyond that, I can’t say.

    But there’s only one time you can be certain that mtDNA and the X chromosome follow the same path: from mother to child.

  3. I have an X match that also shares autosomal DNA with me. I keep my X inheritance chart handy. On Gedmatch it shows my parents are not related. However, when we compared trees I found a match on a paternal line (size of autosomal segment and amount is correct for the paternal match relationship) but that X match was excluded by by the X chart. The X match was small, about 5 cM. Was I correct to conclude the X match could have been “noise?” Should we exclude X under a certain size just as we do with autosomal? I thought X was considered IBD in segments of a smaller size.

  4. FTDNA shows that I have an X-match with another person. I am male. My mother’s DNA is also on FTDNA, and the person does not match my mother. She, in fact, is indicated as matching my paternal side. When I look on the Chromosome Browser, there does not appear to be any matching X-DNA with the other person. Her mother’s DNA is also on FTDNA, and does not show an X-Match, and we believe we know where our match comes from on my paternal side. Am I missing something, or should I assume this is just a mistake in FTDNA’s listing?

    • It sounded like an IBC match until you said that the person shows no x match. I suspect it’s a bug. I suggest you notify FTDNA. Did you drop the match threshold to see if the x match is small? Is so, it’s probably just IBC. They only show an x match ad a secondary match and then no matter how small. If still no match, notify FTDNA.

      • Thank you! Dropping the threshold to 1 cm caused the match to show up with 2.43 matching cms.Mystery explained, and a lesson learned.

  5. Is it possible for endogamy to just show up on the X chromosome? Well over a fourth of my Mom’s 3000 plus matches are listed as X matches at Family Finder with about half of them being over 5 cM, although only about 20 are over 10 cM. Mom’s paternal X-possible great-grandmother was of almost all New Netherland ancestry even though she was born a couple centuries later. There are several of her lines that we know about which end with the same couples, and no doubt more that we don’t. I’ve come to the conclusion that Mom got a big chunk of that concentrated New Netherland X (and I didn’t) and that’s what so many people are matching. Mom’s other X-possibles are German and Scots-Irish but with trees that aren’t quite so convergent.

    • It would be interesting if you could prove whose X you received. I have not seen endogamy displayed only on the X, but that doesn’t mean it couldn’t happen. Are these matches located all over the X or in just one primary region?

      • Sorry it’s taken so long to follow up but I did want to mention that since I’ve started ignoring any segments under 10 cM my X chromosome problems have all but disappeared.. Of the 1300 matching segments my mom has at Family Finder only a couple of dozen are that long. The rest of the 1300 look a lot like the pileups seen on autosomal chromosomes with large numbers of people sharing small segments. My X has similar areas but with about half the number of folks as Mom. Dad has only 140 total segments and even he has a few of those areas. Interesting that three quarters of my X segments of any size don’t match either of my parents, just like most of my small autosomal segments don’t match.

        Out of curiosity I did an X only search at GEDmatch for 20 cM and above and mapped the segments for Mom, Dad and me. The results amazed me. I actually matched my dad on all of them and was able to identify an X-possible common ancestor for two long segments. My mom’s is going to require a lot more work in phasing but at least now I have reasonable clusters to deal with. When I found an X-possible ancestor for a 30 cM segment from two different lines I certainly did a happy dance. Why my mom has all those hoards of matches is still a mystery to me, but at least in a practical sense there is now hope for mapping her X!

  6. Wow and thanks. I understand this a lot better now. As a female with no close relatives to test, but a LOT of genetic “cousins” I know this will help me look at results in a much more informed way. Thanks again. Love the color coding!

  7. Hello, Really, really enjoyed your “X Matching and Mitochondrial DNA is Not the Same” post. Are blank, but colorized, versions of the fans available anywhere? I’ve printed yours out, but writing my own names in is messy. Thanks, Velma Southerland

    • You can print your own chart from your software and color it. You can also download Blaine’s and write your ancestors in the blanks. His aren’t colored with both but you can adapt.

  8. Well written! Thank you! Question regarding the MtDNA. At FTDNA I have a valid MALE “X” match. In fact he is my only valid “X” match. He is also a valid autosomal match. His matrilineal line goes back to a woman with the same birth name as my farthest back matrilineal ancestor. Both women were born in the 1790s in the same general area of NC/VA. His MtDNA group is “U2.” Is that a good indication that I too would be MtDNA “U2”? Dang! I wish MtDNA testing wasn’t so pricy!

    • It’s a good possibility and a very good way to disprove the match or confirm the match which would certainly suggest your matrilineal ancestors share a common ancestor. Good luck!!!

  9. This is very useful! Thank you for this post. I also found that fan charts make it easier to differentiate who passed on the X chromosomes to me and my parents. Thanks to the visuals I created, I now understand where to look at X-matches who match one or the other parent.

  10. Hi Roberta

    Thank you for answering my long searched for question on how many cM’s are needed to constitute an IBD match on the X chromosome.

    On FTDNA I have no X matches 10 cM’s or more. On gedmatch I have 565 X matches 10 cM’s or more. Only 17 are an autosomal match 7cM’s or more. 24 X matches 15 cM’s or more. Only 1 of these is an autosomal match 7cM’s or more.

  11. Hi, Roberta,
    Is it true that an X-match with someone is only valid if there is also an autosomal DNA match with that person on at least one segment of chr pairs 1-22? On GEDMATCH and 23andMe, you can see those types of X-DNA matches, or at least you used to be able to. I’ve always wondered why you would even want to see them.

  12. I’d like to see an analysis of the X chromosome applied to a mirror tree. I would think you could eliminate some descendant lines from the suspected common ancestor?

      • Well if you knew a suspected cousin id’ed from ftdna that was a X match you could build a mirror tree for them in ancestry and attach the target person’s DNA and once potential common ancestor was noted, work forward to eliminate relatives that could not be related based on x match?

  13. Great article. I’m wondering if you could clarify something that is puzzling me if you have time. I have cousins who are the grandchildren of my grandmother’s brother and sister who have tested. I share an X match with my cousin who is the granddaughter of my grandmother’s sister. I don’t share an X match with my cousin who is the daughter of my grandmother’s brother, yet I do share an X match with her daughters and her grandchildren from those daughters. How can that be?

  14. I don’t know where else to ask this, so here goes: which of the major testing companies use the X-chromosome for matching? It’s clear that 23andMe does, based on my matches there. It’s less clear whether Family Tree DNA factors in–although I think not, again based on my matches there — and AncestryDNA is, of course, the great unknown when it comes to DNA matches. I can’t find this information anywhere, but you certainly know a lot more about this than I do!

  15. I’m looking at ftDNA, at matches I have in common with my paternal grandfather. A crap-ton of these matches are also X-matches. Am I understanding correctly that these are all likely to be “noise” and, if not, they must also be matches via another section of the family tree? (I’m female.)

  16. A recent maternal line match and I share the haplogroup X2a2. Just curious whether we would be an x match also.

  17. I’m a co-admin of a FTDNA surname project. One of our members has indicated that they think it would be of great value to the project if we all did mtDNA tests, but hasn’t explained how in a manner that I’m able to understand. Would you be able to explain to me (in simple terms) how that would be of any benefit to our project as a whole?

      • She says, “My suggestion was that if the group took a broader view it would recruit women who have genes from this line the pool is broadened and you may find women such as myself who had a Waugh male ancestor at some point (in my case a great grandfather) and some interesting genealogy that may shine light on the origins of the group. These show up in family finder and the mt DNA of the men who,s mothers also have these genes. Matches with women with their mtdna could be of great interest”. I just can’t follow her reasoning and have no idea what she’s getting at.

        • I think what she is trying to say is that perhaps if the project was open to non Y participants, someone who carries the mtDNA of one of the lines might join.

  18. I am constantly delighted by the clarity of your articles – I had decided that I just wasn’t able to understand about ‘X matches’ – and I’ve ‘heard’ so many conflicting statements about how it works – it is wonderful to now feel like it is understandable. Thank you!!!


  20. Hi! I’m so confused. What if another female rel and I only match (16 cM on 23andMe) on the X, with no other matching? Can I tell where (maternal/paternal side) are we likely to be related? Thank you.

  21. Is it possible for you to make a fan chart and highlight the x match lines for both Y and an MT chart, please?

  22. You share a wealth of meaningful information. I apologize for feeling confused still. I see that i have an X chromosome match with some one on a popular dna test site. I am confident my mother did not birth this female; should I assume that this female and I inherited the x from the same father? 19 of 23 segments of dna match but our percentage is NOT near 25. Hoping you can shed some light. Thank you

  23. I’m a female interested in dna ancestry, one local company has mtdna testing, so i wondered if this testing includes the x chromosome from my dad’s side?

    • MtDNA testing us not autosomal. Also, you need to test at Family Tree DNA to be in their matching data base. Without matching, you’ve missed the power of DNA.

  24. I seem to have matches on both sides of my tree with the same mt Haplogroup (H24a). Plus one of them, is a male who is also an X-Chromosome match to me!
    How can that be?

    Because of this, I have tested with three different companies, one of which was FT’s Full Sequence mtDNA. All three confirm my Haplogroup is correct, and I match the same male, the same way, on the other two sites.

    And no, my parents are not related.

  25. Thanks for a very clear explanation of this topic and especially the graphics. I do have a question about FTDNA results. I have three mtDNA matches – all males – but none are FF matches so no x matches either. I was confused by one of your replies. Should I have a Family Finder match (i.e. x match) no matter how small?? I assumed the match was just too small to identify, which happens with the yDNA matches I handle. Is it possible to have an mtDNA match and no x-match? If so, under what conditions? I haven’t found a way to match chromosomes with anyone other than FF matches since FTDNA changed the Chromosome browser.

    • X and mitochondrial are not at all connected to each other. Having an autosomal match, which includes the X, and a mtDNA match are entirely disconnected. The only time that MIGHT happen is if it’s a relationship within the past few generations. You can have mtDNA matches for many generations into the past since the mtDNA is not admixed like the autosomal DNA is in each generation. You have never been able to match someone on the mt or Y on the chromosome browser. Chromosome browsers (like the one for Family Finder) only work for autosomal DNA.

  26. I have a question about my dad’s X-chromosome matches on 23&Me. He has a male match who shares one large segment of 64 cM. This male match has a female 2C2R who overlaps that segment with 41 cM. I tracked the shared ancestral line of these two matches and it leads back to Connecticut where my dad has a few brick wall ancestors on his maternal line (2xGtGM, 4xGtGF & 5xGtGF/GM). However, neither match shares any autosomal DNA with my dad.

    In addition, a group of sibs (or half-sibs) also match my dad on the same X region for about 50 cM. They also match the the original male match. But again, my dad doesn’t share any autosomal segments with them.

    FYI, my dad’s known maternal second cousins share 48 cM with him on the X. Their cMs are broken into two segments which fall on either side of the one large segment from the unknown matches. The cousins are on FTDNA, so I don’t know if they share any cMs with the 23&Me matches.

    Am I wasting my time chasing these “leads” or not?

    • No, you’re not wasting your time at all. They are great leads and ones you are not getting any other way.

  27. Sorry if this has been answered elsewhere.

    I am male. If one of my DNA matches is NOT an X-match, does that mean that the match is DEFINITELY related to me on my father’s side?

  28. Pingback: X Chromosome Master Class | DNAeXplained – Genetic Genealogy

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