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Not AvailableSnow trout (Schizothorax richardsonii) is one of the economically important coldwater fish, widely used as a food fish in the Himalayan region of India. The present study examined the genetic variations be-tween five geographically isolated populations of S. richardsonii using ATPase 6/8 and COI gene sequences of mitochondrial DNA. Analysis of 25 sequences of ATPase 6/8 gene (842 bp) and 22 sequences of COI gene (847 bp) revealed 16 and 8 haplotypes respectively. The estimated haplotype and nucleotide diversity was high in GR (Gola river, Ranibagh) population (h = 1.00000, π = 0.00475 for ATPase6/8 and h = 0.83333, π = 0.00354 for COI). Results of AMOVA indicated that majority of the genetic variations in both genes are due to variation among populations (65.41 % for ATPase6/8 and 55.57 % for COI gene). The pairwise FST comparison and Neighbour-joining tree revealed low genetic divergence of KU (Kosi river, Uttarwahini) and KR (Kosi river, Ramnagar) population from other populations. The findings of this study showed that vari-ation levels detected by ATPase6/8 and COI gene in population of S. richardsonii were very close to each other and demonstrate utility of ATPase6/8 and COI gene sequences for the population study of S. richard¬sonii for conservation, breeding and management progammes.Not Availabl