A wild and a cultured greenshell mussel (Perna canaliculus) population were compared for biochemical genetic variation at seven polymorphic and four monomorphic allozyme loci. Significant heterozygote deficiencies were observed for all polymorphic loci (La—1,La—2,Lap, Lgg—1,Lgg— 2,Pgi, andPgm) for both populations (except thePgilocus of the wild mussel population). Genotypic disequilibrium was calculated for both populations: genotypic frequencies were significantly non‐random at three pairs of loci among the wild mussels, and significantly non‐random at three different pairs of loci among the cultured mussels. All six pairs of loci which exhibited significant genotypic disequilibrium involved amino‐peptidases, suggesting that these loci form a linkage group, and that neither thePginor thePgmloci are associated with this group. Exact tests for population differentiation based upon population‐specific allele distributions indicated that four of the polymorphic loci were significantly heterogeneous among the two populations, whereas the remaining three polymorphic loci were not. Based upon the private allele system, the number of migrants (Nm) between the populations was estimated to be 2.009, which, according to the private allele system, represents a high level of gene flow. These findings are discussed with regard to the population biology and genetic structure of this species.