The work comprises the analysis of dynamics of vertical distribution and zooplankton structure of the pelagial of the Southern Baikal in 2002. Vertical distribution, as adaptive reactions at various species (and age stages) of the zooplankton during the different periods of thermal stratification was various. During all seasons of year, except summer, a basic species of the zooplankton was E. baicalensis, but in the summer during direct thermal stratification dominated C. kolensis.