Scylla paramamosain (Estampador 1949), a commercially important marine crab species, is naturally distributed throughout the southeastern coastal regions of China. China has a long history (more than 100 yr) for fishing and aquaculture of this crab species (Cowan 1985; Shen and Lai 1994). In the year 2008, the total aquaculture area for S. paramamosain in China has expanded to more than 333 × 106 m2, meanwhile, the yield reached more than 100,000 t. The hatchery-reared crabs exhibited significantly faster growth rate than that was collected from the wild when they were stocked separately, but no significant difference of growth performance between both origins of crabs was found when they were cultured in the mixed ponds (Ut et al. 2007). Maturation and spawning of S. paramamosain are continuous throughout the year with seasonal peaks in certain areas (Vay 2001) and they mate inshore and spawn the eggs offshore. Nowadays, the resource of S. paramamosain has been severely decreasing because of over-fishing and seawater pollution. However, studies about the phylogeography, molecular evolution, and identification of S. paramamosain are limited (Keenan et al. 1998; Ma et al. 2006, 2011; Kitakado et al. 2006; He et al. 2010). Microsatellite markers are thought to be ideal molecular tools for investigations of genetic diversity and inbreeding, parentage assignments, and constructing genetic linkage maps for aquaculture species (Liu et al. 2004; Chistiakov et al. 2006; Ma et al. 2009a; Karlsson et al. 2010; Cheng et al. 2010). By now, only