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¹ ICAR-Central Institute of Fisheries Education, Panch Marg, off Yari road, Versova, Mumbai 400061, Maharashtra, India DOI : 10.4194/1303-2712-v18_5_08 Viewed : 3862 - Downloaded : 2803 Species of genus Setipinna are major contributors in total landings of anchovies. Under the genus, four species have been reported from Indian waters. Among them, Setipinna phasa is a dominant species, distributed in Ganga river system from Allahabad, Uttar Pradesh to West Bengal coast of India. The identity of Setipinna species was found to be ambiguous that needed validation; hence, in the present study, Setipinna species were collected from Diamond harbour and Digha Mohana, West Bengal, India for differentiation based on morphological, meristic and molecular traits. ANOSIM, SIMPER and principal component analysis of twenty three morphometric characters revealed difference among the three variants of S. phasa. While DNA barcoding using mitochondrial cytochrome c oxidase subunit I and 16S ribosomal RNA gene showed very less divergence values (0.00-0.008) among these variants. Further phylogenetic analysis using combined DNA sequences (COI and 16S rRNA) displayed clustering of these variants of S. phasa with significant bootstrap values. Hence the study concludes that even though variants of Setipinna displayed considerable morphological variations, they are not distinct genetically from S. phasa species. Thus the variants of the species seem to be ecotypes of S. phasa and a base in the evolution of others Setipinna species. Keywords : Ecotype, Setipinna, DNA barcoding, India