Knowledge of the genetic diversity and population structure of marine species across their distribution range is essential for the formulation of effective management and conservation strategies. The veined rapa whelk Rapana venosa is a commercially important fisheries resource in East Asia. To provide basic information for fisheries management and artificial breeding, research on the genetic diversity and population structure of R. venosa across the species’ range in China was carried out using 11 microsatellite loci. All of the 11 populations showed high levels of genetic diversity. Shallow, but significant genetic divergences were detected among these populations, suggesting two geographic subdivision groups of R. venosa along the Chinese coast, with nine populations in northern China forming one group and the other two populations (Rizhao and Zhoushan) forming another. A significant isolation by distance pattern was observed in this species (r = 0.412, P = 0.012), indicating that isolation by geographic distance may play an important role in population differentiation. These results could provide valuable genetic information for the fishery management of R. venosa.