Pink anemonefish (Amphiprion perideraion) has commercial value as a popular aquarium fish and due to its collection from the wild there are concerns for the conservation of the species. Six polymorphic microsatellites were used to reveal population genetic structure of pink anemonefish from three locations (Quang Nam, Khanh Hoa – Ninh Thuan and Phu Quoc) in Vietnam. Analyses showed evidence for high levels of gene flow among populations sampled from the South China Sea (FST = 0.008, P > 0.05). Genetic homogeneity of A. perideraion in this region is likely due to the oceanographic-driven interaction of pelagic larvae in central waters off Vietnam. In contrast, strong genetic structure was evident among the South China Sea and Gulf of Thailand populations (FST = 0.131 – 0.146, P < 0.01). This high genetic differentiation between the South China Sea and Gulf of Thailand populations suggests that the sustainable management of this species in Vietnam needs to be enacted according to indigenous need as a two separate stocks.