The GY population differed greatly from the other four northern populations despite GY not being very far away from them geographically, and this can also be explained by the effects of ocean currents. GY is located at the junction of Shandong and Jiangsu Province where ocean eddies exist (Fig. 1), which may reduce gene exchange with other populations outside the vortex. This has been seen in studies of population differentiation of Mactra chinensis (Ni et al., 2011). In addition, GY is located in Jiangsu Province where a large area of beach exists. The existence of beach may limit genetic communication given the caving habit of O. minor. Geographic distance among the YT, RC, DL, and LZ populations is small, but there is greater genetic distance between LZ and the other three populations. This could be affected by the complex hydrology and bathymetry in Bohai Sea and Yellow Sea. LZ is located in the Bohai Sea, which is a semi-enclosed sea, so it is likely less genetic exchange takes place between the LZ and Yellow Sea populations given the limited dispersal ability. Similar findings had also been seen in the population genetic study of the other benthic marine organisms with a short pelagic larval duration (Zhan et al., 2009; Ni et al., 2011).