The Portuguese oyster, Crassostrea angulata, is one of the most important shellfish species in China andoccurs mainly in the intertidal zone of the south Yangtze River. It is widely cultured in Zhejiang and Fujian provincesand many of its seeds are collected from natural areas. Molecular genetic data can provide valuable insightsinto C. angulata management and conservation. In the present study, we investigated the population geneticstructure and demographic history of C. angulata from the coast of Zhejiang (Yueqing) and Fujian (includingNingde, Langqiao, Fuqing, and Putian) provinces by analyzing the partial mitochondrial cytochrome c oxidasesubunit 1 (CO I) sequences in 183 samples. All populations were characterized by high genetic diversity.Forty-four polymorphic sites were identified, and 39 haplotypes were found. The mean genetic and mean nucleotidediversity values were 0.8524 and 0.00406, respectively. Despite high levels of genetic diversity within thepopulations sampled, no significant genealogical branches corresponded to the sampling locality. Analysis of molecularvariance indicated that most of the genetic variation was attributed to within-group variation (91.94%,P=0.0003). Population pairwise ΦST values were low (ΦST = −0.01193~0.11486), suggesting frequent gene flowamong the populations in this area. However, low but significant genetic differentiation was observed between theNingde samples and the other four samples from four sites, which was presumably due to the relatively closedgeophysicallocation of Ningde. Ningde is surrounded by many bays, islands, and gyres, which act as natural barriersthat may have hindered dispersal of oyster larvae. The haplotype network of CO I sequences with stellateradiation structure suggests no clear geographical differentiation. A Bayesian phylogenetic tree was characterizedby a staggered distribution of haplotypes and some small branches supported with moderately high bootstrap values.Significant expansion of C. angulata populations is suggested based on results from neutral tests and themismatched distribution; the actual time that expansion likely started in 2.5×105–2.1×105 years ago. Historicalrecolonization (though population range and demographic expansion during the late Pleistocene) and the currentgene flow (larval dispersal interacting with oceanographic processes, such as ocean currents) of adult sedentary C.angulatamay be responsible for the poor genetic differentiation. Our results will help in understanding the historicalprocesses of intertidal species and help disentangle the complex interactions among various factors thatgenerate the phylogeographical patterns and genetic diversity of C. angulata in the East China Sea.