One consumer vendor of DNA testing, Family Tree DNA, when they notify their customers of a match by email state:
When comparing the Hyper Variable Regions 1 and 2 of your mtDNA, a match has been found between you and another person(s) in the Family Tree DNA database. Matches of the mtDNA have more Anthropological significance as the time frame for a common ancestor could go beyond the Genealogical time frame.
Anthropological time for human mitochondrial DNA is essentially from about 200,000 years ago to the present. It is measured in age with relative measurements like carbon 14 testing rather than history.
The Genealogical time frame is the last portion of that since the beginning of the use of surnames. The extreme end of that is about 1000 years ago beginning with tracing lineages in royalty.
The formation of surnames began about 900 years ago and did not become common until about 400 years ago. James the Baker became James Baker. Fred the Blacksmith may have become Fred Black or Fred Smith.
Y Chromosome DNA, is passed on with a typical mutation rate of .02% or two in 10,000. As it is passsed by the male lineage, it tends to represent a paternal lineage that begins with a few mutations that coincide with the formation of surnames.
This is unlike the autosomal DNA used by the FBI which changes with each individual offspring and is a combination of genes from both parents.
Mitochondrial DNA (mtDNA), on the other hand, is passed from mother to daughter in the maternal lineage with a lower rate of mutation than the yDNA. While it is also passed from mother to son, that son does not pass his mtDNA to his offspring.
In one case, mtDNA of a 9,000 old "Cheddar Man" in the United Kingdom was traced down to a current resident of the UK teaching school in the area where Cheddar Man was found.
So, while two individuals may have the same mtDNA, it does not confirm they have a common ancestor within the timeline that surnames and genealogies have existed. If two individuals do not have the same mtDNA, therefore, it does exclude that possibility of a common ancestor.
The "Hyper Variable Regions" of the mtDNA are areas where the most, but not only, change occurs. The mtDNA can be thought as a circle or loop which breaks at the top during the process of reproduction.
The mitochondria are separate from the chromosomes and reproduce independently of them. There can be hundreds of mitochondria within one individual cell. Since there are so many copies of a relatively small chain of DNA, it is more easily tested.
Not all mtDNA testing is alike. For comparison, a full genome of mtDNA in humans is normally 16,569 base pairs of DNA. It is extremely small in comparison with the millions of base pairs in a single chromosome, of course. Consumers can have this tested for less than $500.This level of testing does give a level of resolution that indicates a particular maternal lineage.
Region one can be tested for less than $200 and both regions can be tested for less than $300. However, the testing done on both of the Hyper Variable Regions by consumers only covers only 1143 base pairs of that 16,569 base pairs. You could have differences outside those Hyper Variable Regions that occured over 60,000 years ago that are not detected by such testing. This level of testing does not give a level of resolution that indicates a particular maternal lineage.
However, this level of resolution is greater than the 721 base pairs used by the FBI. The mtDNA testing by the FBI is useful for exclusion if suspects, but it cannot be used to identify an individual as the one in an evidence sample.
Even if there is a "match" at that level of resolution, the suspect and the one the evidence sample came from could be not only separate individuals, but not even related for tens of thousands of years.
So, the use of mitochondrial DNA testing has its limits in genealogy and certainly in the courts.