The population structure of Epischura baicalensis Sars (Copepoda, Calanoida), one of the key endemic species of the plankton community of Lake Baikal was studied. An analysis of mitochondrial DNA polymorphism revealed no genetic differences between Epischura sampled in the different basins of the lake or in the winter-spring/summer generations. Baikal Epischura is represented by a single panmictic population with a high level of mtDNA haplotype diversity.