The Asian green mussel Perna viridis is an abundant and important ecological and economical species across its native range. However, outside its native range, this species has been considered invasive and concerns have been raised worldwide regarding its potential impacts. Despite this, little work has been done to investigate the genetics of native and/or introduced populations of this species. In the present study, we developed 16 new polymorphic microsatellite markers using the Illumina MiSeq Platform. Four to 15 alleles per locus were detected. There was no evidence of linkage disequilibrium between pairs of loci and all loci were in Hardy-Weinberg equilibrium.