Truss network analysis and protein gel electrophoresis were used as tools to fund out intraspecific differences between Nemipterus mesopn'on populations collected from the marine landings of Chennai and Kochi. Truss morphometric studies showed morphologically homogenous populations. Marked differences in allele frequencies between the two populations were not evident in protein electrophoresis. Average heterozygosity values for Chennai and Kochi populations were 0.643 and 0.718 respectively. One out of the three loci in the populations showed significant deviations from Hardy - Weinberg equilibrium. Genetic identity and genetic distance values were 0.99962 and 0.0038 respectively. Electrophorestic results confirmed morphological conclusions.