For the first time data on the taxonomic composition and structure of zooplankton in two morfolimnically different thermokarst lakes from Chkalov lake group in Chara depression are provided. The morphological and hydrological characteristics of lakes, zoogeographical and ecological characteristics of species are given. Quite high species similarity of zooplankton in examined lakes and other reservoirs of Chkalov group is revealed. The species diversity index higher in the shallow littoral lake than in the deep littoral-profundal one. It is shown that the abundance and biomass in June-July in the deep lake is dominated by copepods, and in the littoral one – rotifers and cladocerans. The dynamics of quantitative zooplankton characteristics (abundance, biomass) in morphometrically different lakes is not match. Thus, it is revealed that the taxonomic structure of zooplankton depends on the morphometry of lakes.