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¹ Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar-751002, India DOI : 10.4194/1303-2712-v21_1_02 Viewed : 2306 - Downloaded : 2138 Clarias magur, popularly known as magur, is one of the economically important catfish species having high aquaculture potential in India due to its efficient food conversion, taste, and nutritional benefits. Due to habitat degradation, over exploitation, lack of resources, indiscriminate use of agricultural pesticides and introduction of competitor exotic species, the wild populations are dwindling day by day. According to IUCN, it is listed as endangered species. In the present study, the population genetic structure of 206 magur samples collected from seven different geographical regions was examined using partial mitochondrial D-loop (control region) sequence variation. In total of 17 haplotypes were observed with high number of private alleles, number of haplotypes ranged from 2 to 6 and maximum number of haplotypes was observed in UP population. Haplotype diversity and nucleotide diversity ranged from 0.06897 to 0.76322 and 0.00019 to 0.00208, respectively. Pairwise FST values ranged from 0.01383 to 0.62069 and highest genetic differentiation was observed between AP and AS population. Low genetic diversity and significant population genetic differentiation was observed in the present study. The information generated in the present investigation would facilitate formulating appropriate strategy for management, conservation, and genetic improvement program of this commercially important aquaculture species. Keywords : Genetic Diversity, Genetic Differentiation, Private Allele, Haplotype Diversity, Nucleotide Diversity