Search for conditions of molecular genetics analysis aimed to obtaining of maximal diversity of intestinal microflora genetic pools in fish (black Baikalian grayling) was performed. We analyzed the influence of both main methodological and of some ecological factors onto the diversity and the composition of the genetic pools obtained. Methods of extraction of total DNA and conditions of polymerase chain reaction was varied. Probable impact of habitat conditions (natural water bodies and aquariums) and peculiarities of structural and functional organization of different intestine segments in fishes were investigated. Conditions for obtaining of maximal genetic diversity of intestinal microflora organisms of black Baikalian grayling are determined.