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¹ National Institute of Oceanography, Biological Oceanography Division (BOD), Dona Paula, Goa 403004, India DOI : 10.4194/1303-2712-v12_4_17 Viewed : 4661 - Downloaded : 3682 Frigate tuna (Auxis thazard) is an epipelagic, neritic as well as oceanic species. In present study, genetic variation was surveyed using PCR-RFLP of mitochondrial DNA D-loop region to test for the presence of stock structure of frigate tuna along the Indian coast. A total of 364 individuals were sampled from eight major fishing zones along the Indian coast. PCRRFLP analyses of D-loop revealed significant genetic heterogeneity between samples of Port-Blair and rest of the Indian coast. Population genetic structure was also corroborated by significant value of global test of population differentiation among samples (P = 0.01). Therefore, the null hypothesis of single genetic stock of frigate tuna along the Indian coast can be rejected. The results of present study suggest the two genetic stocks of frigate tuna across the coastal waters of India. Keywords : Genetic variation, Indian waters, composite morph