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¹ National Institute of Oceanography, Dona Paula, Goa 403004, India DOI : 10.4194/1303-2712-v12_3_02 Viewed : 4389 - Downloaded : 2885 Kawakawa Euthynnus affinis is an epipelagic migratory tuna species, widely distributed in the tropical and subtropical waters of the Indo-Pacific region. It constitutes the largest tuna fishery in Indian waters. In present study, restriction fragment length polymorphism (RFLP) analysis of the mitochondrial D-loop region was employed to examine the levels of genetic diversity among kawakawa samples collected from eight main fishing zones (Veraval (VE), Ratnagiri (RA), Kochi (KO), Kavaratti (KA), Port-Blair (PB), Tuticorin (TU), Pondicherry (PO) and Vizag (VI)) along the Indian coast. A 500 bp segment of mitochondrial D-loop region was screened in 400 samples using six restriction enzymes (Rsa I, Alu I, Hinf I, Hha I, Msp I and Hae III), resulting in 13 composite morphs. Analysis of molecular variance (AMOVA) of mtDNA data revealed no significant genetic differentiation among sites (F_ST = -0.00446, P = 0.84946). Results of the genetic analyses of present study suggest the single stock of kawakawa along the Indian coast. Keywords : PCR-RFLP, mtDNA, D-loop, Indian waters