Variation in mitochondrial DNA is often used to trace the evolutionary history of populations and species. We here discuss the effect of infection with cytoplasmically inherited male-lethal symbionts on mitochondrial genome evolution. Male-lethal symbionts spread when killing male hosts increases the lifetime reproductive success of sibling female hosts. This increase in the survivorship of daughters from individuals bearing a male-killer will produce a concomitant increase in the frequency of mitotypes associated with the male-killer. If horizontal transmission of the microoorganism is rare and population sizes not very small, then linkage disequilibrium between microorganism and particular mitotypes will result in a reproduction of within-population mitochondrial variability both because of a selective sweep during the spread of such a micro-organism, and also at equilibrium. Male-killing symbionts may thus confound the use of mtDNA variability in estimation of population parameters. We discuss the differences between the effects of male-killers and the cytoplasmic incompatibility-inducing symbiont Wolbachia, and the possibility that estimation of gene flow between populations may also be confounded by symbiont presence.