Two coeval assemblages of fossil fishes came from the middle–late Miocene deposits of Sakhalin Island, Russia. The fish community from the Agnevo Formation consists of 28 species belonging to 15 families of shallow-water fishes, with the predominance of cottoids, stichaeoids, and pleuronectoids. The assemblage from the Kurasi Formation contains fossils of 35 species from 27 fish families and comprises mainly mesopelagic dwellers, such as myctophids, argentiniforms, stomiiforms, and aulopiforms. These assemblages differ mainly in the number of species belonging to extinct genera. Among the 28 fish genera known from the Agnevo Formation, 14 (50%) genera are extinct. In contrast, out of 35 genera described from the Kurasi Formation only three (about 8.6%) genera are extinct. The morphological distances between the fossil and recent congeneric species are more pronounced and defined in the shallow-water community than in the deep-water assemblage. The differences in taxonomic composition between the fossil assemblages likely reflect the different influence of the climatic and geographic events in the Neogene and Quarternary on the evolutionary rates of shallow- and deep-water fish communities.