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Fishes constitute about half of all known vertebrate species and have colonized nearly all available marine and freshwater habitats. The greatest diversity of fishes is found in the marine realm as well as in large (and often old) freshwater lakes such as the East African Great Lakes. Here, we compare the phylogeographic history of fishes in marine and large freshwater ecosystems, with particular emphasis on groups that underwent adaptive radiation, i.e. the emergence of a multitude of species from a single ancestor as a consequence of the adaptation to different ecological niches. Phylogeographic analyses are highly suited to identify and compare causal agents of speciation in rapidly diversifying groups. This is particularly true for fishes, in which distribution ranges and preferred habitat structures can be quantified in a straightforward matter.
