In the present study three species of mackerel, Rastrelliger present in Indian waters were taken for genetic identification using cytochrome c oxidase subunit I and 16s rRNA sequences. Accurate identification of these species is important for fishery management as its morphological characters are very similar. In this study, the sequences of COI and 16S rRNA were determined from 19 individuals of three Rastrelliger species, Rastrelliger kanagurta, Rastrelliger brachysoma and Rastrelliger faughni from Andamans and Indian mainland to study the phylogenetic relationship. The intraspecies and interspecies genetic distance ranged from 0.000 to 0.002 and 0.007 to 0.015 respectively based on 16S rRNA sequences. Using COI data analysis, the intraspecies genetic distance ranged from 0.000 to 0.012, while it varied from 0.039 to 0.086 for interspecies. The present study clearly demarcates three species of mackerel based on the mitochondrial genetic sequences and also showed a non-descriptive genetic distance of R. kanagurta from mainland and Andaman Islands.