The article presents the results of morphometric and molecular genetic studies on the fish species Cottus jaxartensis collected from the Ugam River of the watershed of the Chirchik River (Uzbekistan). The material used was 6 fish samples, with 57- 84mm long (average 73.5). The numbers of rays are ID 7-8 and II D 17-18 on the dorsal fins, ventral (V) 5, pectoral (P) 14-15, anal (A) 12, caudal (C) 17-18; the number of pores on lateral lines are 34-36; the coefficient of variation of plastic features is varied up to 0.4-19.2% (average 7.8 % ), of which signs o, io, H, h, lca, hD, lP, io/c have high variability, and the rest of the characters had medium and low variability. A comparative study of the nucleotide sequence of the 16S gene of mtDNA of the species C. jaxartensis with the nucleotide sequence of the species C. ricei was carried out from GenBank of the National Center for Biotechnology Information. Between the nucleotides of the 16S region of mtDNA in the species C. jaxartensis and the species C. aleuticus and C. gobio, there are differences of 6 nucleotides, and the difference with the total number of nucleotides is 1.8%; with species C. asper, C. marginatus, C. perplexus, C. poecilopus, C. pollux and C. volki between 9 nucleotides (2.7%); with species C. bairdii, C. beldingii, C. gulosus and C. szanaga between 12 nucleotides (3.6%); with species C. cognatus, C. pitensis and C. reinii between 11 nucleotides (3.5%). The 16S gene of the mtDNA nucleotide sequence data was first placed in the GenBank, and the accession number OR470689 was obtained.