Perna viridis (Linnaeus, 1758) the Asian green mussel, belonging to the family Mytilidae is widely distributed in Indian subcontinent. The species is native to the Asia-Pacific and possess importance in molluscan fishery in this region, and also considered as an ideal candidate for aquaculture, due to its high nutritional value and faster growth rate. The global capture production of the species exhibits considerably declining compared to aquaculture production. The global capture production of P.viridis was 1, 65,500 tonnes in 1971 to 4042 tonnes in 2014; whereas the aquaculture production was 1, 59,474 tonnes in 2014 (FAO, 2017). In India, capture production of P.viridis formed 5.27% (7085 tonnes) of the annual bivalve production (1, 34,235 tonnes) (CMFRI, 2016). For sustaining capture production of the species, genetic information on wild populations is essential. Moreover, the knowledge of demographic processes of a species is essential for the development of responsible hatchery production of a species, sustainable aquaculture and other conservation strategies. Earlier studies by Divya et al. 2017 revealed distinct stock structure among P.viridis population along Indian coast using mitochondrial markers. In the present study, genetic variation and population structure across the distribution of this species from Indian peninsula were assessed using the microsatellite marker panels of 15 loci. A total of 37 polymorphic microsatellites identified in P. viridis were screened { 8 loci from Cao et al. (2013), 10 loci from Lin et al. (2007) and 19 loci from Ong et al. (2009)} in the collected specimens from different locations and multiplex panels of 15 loci were designed considering secondary structure using Oligo7 and Autodimer softwares. The total number of alleles per locus ranged from 11 to 33 and the allele size ranged from 120 to 390 bp. Mean value of observed heterozygosity (Hobs -0.741) for all populations was low compared to the expected heterozygosity (Hexp- 0.75). Populations were found in HW equilibrium for majority of the loci. Genetic stock identification using Structure software; AMOVA and pair-wise FST analysis using Arlequin software, exhibited two distinct stocks - one along the west coast (Arabian Sea) and other along the east coast (Bay of Bengal). No significant pairwise genetic distance was noted among east coast population (0.004, P>0.01), whereas very low but significant pairwise Fst was observed among west coast populations (0.019, P<0.01). Bottleneck analysis indicated genetic stability of species in the wild. P. viridis being an aquaculture important species, the findings of the present study strongly suggest the need for adoption of stock specific rehabilitation and relaying programmes of the species from Indian waters.