Microbiological and chemical research of аutochthonous microbial communities of the wastes of heap leaching showed that biodestruction of cyanides and thiocyanates could occur under alkaline conditions. In this case, their content is 260 ppm and 150 ppm, respectively. The diversity of dominant representatives of microbial associations which are able to destruct cyanide-bearing compounds was determined in accordance with 16S rDNA and is presented by species of Hydrogenophagа and Pseudomonas. The optimization conditions of cultivation and biotechnological potential of аutochthonous microbiota from the wastes of heap leaching are discussed.