A spectacular adaptive radiation of crustaceans has occurred in the Black, Caspian, and Aral seas. This study tests several evolutionary scenarios based on the extent of genetic differentiation and the phylogenetic relationships among endemic mysids and gammarid amphipods from the Black and Caspian seas. Molecular phylogenies for these taxa were based on two mitochondrial genes: cytochrome c oxidase subunit I and the large ribosomal RNA subunit (16S), and one nuclear gene, the large ribosomal RNA subunit (28S). The results support the monophyly of the Ponto–Caspian gammarids (genera Dikerogammarus, Echinogammarus, Obesogammarus, and Pontogammarus), suggesting their origin from one colonization event. By contrast, several colonization events preceded the radiation of the Ponto–Caspian mysids (genera Limnomysis and Paramysis). Levels of intraspecific divergence were variable, with mysids showing either no geographic structure or deep genetic splits reflecting a long history of reproductive isolation between populations in marine settings and those in fresh waters. These findings suggest that the diversity of the Ponto–Caspian crustaceans has been underestimated and that species regarded as euryhaline are often composed of distinct evolutionary groups whose taxonomic status should be reevaluated.