The mitochondrion and its genome - with its unique set of mutations -are inherited in a maternal lineage. Thus, females in a family - from grandmother to mother to daughter - all share identical mt chromosomes. Male children share a common mitochondrial genome with their mother and female siblings. Fathers make no contribution to the mitochondria of their male or female children.

Consider the sperm and egg at the moment of conception. The mammoth egg is endowed with perhaps 100,000 mitochondria. The tiny sperm's mitochondria (perhaps 50-100) are concentrated at the base of the tail, where they provide energy to power the flagellum. Very few male mitochondria are believed to enter the egg at the moment of conception, and those that do can easily be lost by "dilution" when the egg cytoplasm is partitioned during mitosis. Moreover, there is evidence that any remaining male mitochondria are actively eliminated from the egg. It appears that ubiquitin, expressed on the mitochondria surface, marks the male mitochondria as "foreign" and targets them for destruction.

The lack of paternal chromosomes with which to recombine, greatly simplifies the analysis of mitochondrial inheritance. The mt genome is inherited intact over thousands of generations, without the confounding effect of crossover with a paternal chromosome. Although new mutations occasionally arise in a lineage, they are few and easy to discern. Because the mt genome is haploid - having only a contribution from the mother - mt DNA types are termed haplotypes.