The population structure ofRastrelliger kanagurta (Cuvier 1817) from two localities off Goa (Arabian sea) was assessed from genetic and morphological characters. Seventeen loci were examined from 8 enzymes, sarcoplasmic proteins and hemoglobins. The allele frequencies were not significantly different between the two localities. Nei’s genetic distance value was 0-0017. The proportion of polymorphic loci at the 1% level was 47-1 and 52–9%. The level of genetic variation, estimated by average observed heterozygosity, was 5–8 and 6–6%. The sarcoplasmic protein-2 locus was found to be highly polymorphic. Significant (P< 0-001) departures from Hardy-Weinberg expectations were observed at this locus. About 67–89% of the variation in meristic characters was found to be within the groups.