The fish fauna of Lake Onego is ecologically heterogeneous, composed of three major groups of species: psychrophilic, relatively thermophilic and background fishes. Drawing upon the combined analysis of the fish ecology, species composition of the fish population in the lake (as well as in adjacent basins) and palaeolimnological materials the following scheme of emergence of the fish species groups was outlined. The species arrived in two major waves. The first, most ancient one comprised cold-water (Eemian relicts) and some background species. They arrived here in the Late Glacial, when there existed the South Onego periglacial lake. The second, younger wave of arrivals is represented by relatively thermophilic species (immigrants from the Volga and Caspian areas). They penetrated the lake in the pluvial period of the Holocene climatic optimum from the Upper Volga water system via the Lake Beloye catchment, either directly or (more likely) via the Onega River watershed.