An electrophoretic survey of allozyme variation was conducted in four, highly polymorphic loci on nine populations of ostracod Candona neglecta Sars from three different environments: the profundal of post-glacial lakes, deep muddy bottom of the Baltic Sea and small astatic water bodies. The results suggest lack of genetic isolation between populations from lake profundal and the Baltic Sea. On the other hand a very distinct founder effect can be noted in the case of young, isolated populations from small astatic basins. It is suggested that a population inhabiting a large lake may be genetically subdivided due to differentiated eutrophication.