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Mischief Reef is located in the eastern Nansha Islands of the South China Sea. With increasingly intense anthropogenic disturbance, Pinctada fucata, a previously unrecorded species in the reef, has occurred in the region. In this study, we identified and described the occurrence of P. fucata in Mischief Reef based on morphology and molecular markers. Furthermore, we performed a population genetics analysis of seven P. fucata populations of the South China Sea. All P. fucata populations showed significant high-level genetic diversity, but the differentiation among P. fucata populations was small. There was an FST value close to zero (−0.0083) between the Lingshui and Mischief Reef populations. Our results hint that Lingshui may be one of the potential sources of P. fucata to Mischief. In addition, we discussed the possible cause of the mass occurrence of P. fucata. The present study serves as a warning that anthropogenic disturbances have disrupted the local ecosystem in Mischief Reef.

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