Genetic diversity and population structure of the Asian green mussel Perna viridis in South China Sea based on microsatellite markers

•Moderate genetic diversity among Pernaviridis populations.•Low and non-significant genetic divergence among P. viridis populations.•Oceanic currents and long planktonic larval stage may homogenize populations.

The green mussel, Perna viridis is ecologically and economically important in the coastal region of the South China Sea. Determining its population genetic structure at this fine geographic scale will help sustainable management of natural stocks. In this study, we examined the genetic diversity and population genetic structure of P. viridis from four locations in the South China Sea (n = 45–48) using nine microsatellite loci. The results showed moderate levels of genetic diversity in all four samples (mean A = 13.222–14.000, mean Ae = 7.092–7.571, mean Ar = 12.894–13.746, mean Ho = 0.596–0.656, mean He = 0.690–0.733) and a large effective population size estimate for the pooled sample (total Ne estimates = infinity, 95% CI = 1869.0-infinity). We did not detect any sign of recent bottleneck events in P. viridis populations in the South China Sea. The conventional and a model-based analysis reveal low, non-significant genetic divergence among the four samples (FST = − 0.001–0.005, P > 0.05/6). The results obtained from this study can provide valuable genetic information for the conservation and fishery management of P. viridis by retaining the high Ne estimates.