The article provided information about nine species, which belong to the Cladocera order in lakes of different sizes and ecological conditions, including Lake Davut, Lake Akcha, Lake Qorateren, and Lake Saykol in the Republic of Karakalpakstan and seven species in the lakes of Fergana Valley. Daphnia galeata found in Akcha and Sariqamish lakes was identified by molecular genetic methods and proved to be a new species in the Republic of Karakalpakstan. During the conducted studies in the lakes of the Republic of Karakalpakstan, 2 species of Cladocera were recorded in Lake Akcha, 3 species in Lake Qorateren, 2 species in Lake Davut, 7 species in Lake Saykol. Whereas, in the Fergana Valley, 9 species were determined in Lake Sariqamish, 5 species in Lake Toda, 2 species in Lake Ettikol, and 3 species in Lake Kolgandaryo.