Rates of molecular evolution in eight protein-coding mitochondrial genes from two parallel lineages of Baikalian amphipods were compared to those in the representatives of gen. Gammarus. In six genes (Atp6, Cox2, Cox3, Nad1, Nad5, Nad6), there was a significant acceleration in the evolutionary rate of Baikalian species over those from Gammarus group. Correlation of the absolute rate of base substitution accumulation and the acceleration was insignificant, that allowed us to propose mostly adaptive reasons for the effect found.