The hard-shelled mussel, Mytilus unguiculatus, is one of main aquaculture bivalve species in Southeast China Sea, and excellent growth characteristics. For mussel breeding, farmers use wild individuals to multiply the cultured populations. However, blind selection of wild parents has inevitably resulted in inbreeding and decreased genetic variation. In this study, four wild specimens groups (ZSW, WZW, NNW, and FZW) and four cultured specimens groups (ZSC, WZC, NDC, and FZC) of M. unguiculatus were used to analyze their genetic diversity, population structure and understand the relationship between the wild and cultured specimens groups. The results showed that haplotype diversity (h) of the cultured specimens groups (from 0.621 to 0.797; average, 0.717) was higher than that of three wild specimens groups (ZSW, WZW, and NNW; from 0.428 to 0.668; average, 0.560). The pairwise FST values suggested that only the FZW sample showed significant divergence from the others. The wild and cultured ZS and WZ specimens groups were similar, and the wild and cultured ND specimens groups were crossed. Thus, we need to establish genetic protection units for M. unguiculatus, limit the selection of breeding parents, and maintain a high-quality germplasm bank for M. unguiculatus.