For studying of microbiocenoses, microbiological investigations of industrial solutions PR, BP, CNS and settling reservoir № 6 of Kanzhugan deposits for detection and isolation of hemolitautotrophic bacteria of four physiological groups, which under theoretical assumptions could promote underground bacterial leaching of uranium, was carried out. These sulfate-reducing and denitrifying bacteria A.ferrooxidans and A.thiooxidans. In the process of study of microflora of uranium deposits of Southern Kazakhstan were guided by two positions: 1) study conditions of development of microorganisms, and also 2) find out and consider microorganisms, which are «selected by the environment». Therefore, the degree of microbial activity in the ecosystem determined based on their number and chemical analyses of samples. Also, experiences with cultures А.ferrooxidans and А.thiooxidans, which played a significant role in uranium oxidation, have been performed.