Abstract: The purpose of this study was to analyze the genetic and species heterogeneity of lactic acid bacteria ( LAB) from the intestinal tract of cold-water fishes in the Eerqisi river of Xinjiang and Heilong River, which lay the foundation for exploitation resources of lactic acid bacteria.Psychrophilic LAB isolated from cold-water fishes intestinal tract by using MRS, Elliker, M17 culture medium, and measured its optimal growth temperature. According to 16 S rRNA gene sequences preliminarily to determine the phylogenetic relationship of psychrophilic LAB, those highly homologous strains was based on rep-PCR fingerprint to further distinguish.It was obtained that 134 psychrophilic LAB from the gastrointestinal tract of cold-water fishes, and the optimum growth temperature was 15²4 ℃.The sequencing results indicated that the selected psychrophilic LAB were divided into seven genus: Lactobacillus, Lactococcus, Enterococcus, Streptococcus, Leuconostoc, Weissella, Carnobacterium 7 genus, 19 species, respectively, and the dominant bacteria was Lactobacillus. Rep-PCR fingerprint showed that there was a different degree of genetic difference, not only in the same genus of lactic acid bacteria of different species level, but also among various strains of a specie.