Development of microbial biota of the region of the Southern Aral Sea, which characterized by excessive aridity and salt concentration and presence of pesticides’ traces as well, was studied. It was established that analyzed natural microbial biota comprises sporogenous, ammonifying and oligonitrifying microorganisms as well. Nitrifying and denitrifying microorganisms were not revealed. Filamentous fungi belonging to genera Aspergillus, Penicillium, Cladosporium were isolated as well. At the same time, nitrifying and denitrifying microorganisms were isolated from arable soils, where humus content is higher. Strains of Azotobacter, resistant to mixture of pesticides, were isolated as well.