The Asian green mussel (Pernaviridis) is a bivalve species with a high economic value. The waters surrounding the Malaysian state of Sabah hosts a wide range of geographically distributed populations of P. viridis whose population structure is unknown. This study was conducted to elucidate the genetic diversity and population structure of Asian green mussel from six sites located along the coastline of Sabah based on the mitochondrial DNA control region (D-loop). The complete D-loop sequences of 197 individuals were recovered by amplification using PCR, followed by DNA sequencing. Interpretation of the results revealed that the P. viridis populations exhibited high haplotype diversity (H d =0.912±0.0002) and low nucleotide diversity (π=0.00890±0.00066). The AMOVA analysis showed  ST was 0.02322 (P value<0.05), which is indicative of low but significant structuring. Pairwise ST ranged from low to moderate indicating population differentiation. Five out of the fifteen population pairs showed significant population differentiation. Both AMOVA and pairwise  ST suggest there were significant population subdivisions in Asian green mussel population in Sabah. Although the Asian green mussel population in Sabah has gone through a severe mass mortality, evidence for genetic bottleneck was not detected. However, a smaller population size after a severe demographic reduction can cause the population become vulnerable. Thus, regular monitoring of Asian green mussel population is required to keep track of fluctuations in population size and composition. This study provided new population genetic information which is crucial for establishing fisheries management strategies for this species.

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