Several recent population-level studies of mitochondrial DNA (mtDNA) variation in Tanganyikan cichlid fishes illustrate the strength and utility of mtDNA analysis as a powerful tool in evolutionary biology. This chapter attempts to show that these studies also contain information about the various levels of biodiversity that are relevant for the identification of "evolutionary significant units" (ESUs) and the assessment of conservation priorities of cichlid taxa or areas from an evolutionary perspective. These results based on mtDNA studies on cichlid populations are consistent with the notion that species should never be viewed as undifferentiated monotypic entities. The presence or absence of genetically and geographically distinct populations is an important feature that characterizes each of these species, and is important to consider when arriving at informed conservation or management decisions.

Mitochondrial DNA studies have also provided new information on the distributional boundaries of some genetically divergent cryptic species, a conclusion that, in a number of examples, has been supported by the subsequently discovery of morphological and behavioural differences. It is possible that there may be many more undiscovered cases of allopatrically occurring morphologically similar fishes that are erroneously considered to be conspecific.