Genetic structure of skipjack tuna Katsuwonus pelamis from the Indian region was investigated using sequence data of mitochondrial DNA (mtDNA) D‐loop region. A total of 315 individuals were sampled from six major fishing grounds around the east and west coasts of India
including the Andaman (Port Blair) and Lakshadweep (Minicoy) Islands. Nucleotide and gene diversities were high in all the sample collections. Significant genetic heterogeneity was observed for the mtDNA sequence data among sites (φST = 0·0273, P < 0·001).
Analysis of molecular variance (AMOVA) showed significant genetic variation among four groups (φCT = 0·0261, P < 0·05) which was also supported by spatial AMOVA results. The null hypothesis of single panmictic population of K. pelamis along
the Indian coast can thus be rejected. Phylogenetic analysis of the mtDNA sequence data showed the presence of four clades of K. pelamis in the Indian waters. There was no clear pattern, however, of haplotypes and geographic location among samples. The results of this study suggest
the occurrence of four genetically differentiated groups of K. pelamis across the coastal waters of India.