The swimming crab,Portunus trituberculatus, is one of the main aquaculture species in Chinese coastal regions due to its palatability and high economic value. To obtain a better understanding of the genetic diversity ofP. trituberculatusin the Bohai Sea, the present study used 40 SSR loci to investigate the genetic diversity and population structure of 420P. trituberculatusindividuals collected from seven populations in the Bohai Sea. Genetic parameters revealed a low level of genetic diversity in the cultured population (SI= 1.374,He= 0.687, andPIC= 0.643) in comparison with wild populations (SI≥ 1.399,He≥ 0.692, andPIC≥ 0.651). The genetic differentiation index (Fst) and gene flow (Nm) ranged from 0.001 to 0.060 (mean: 0.022) and 3.917 to 249.750 (mean: 31.289) respectively, showing a low differentiation among the seven populations ofP. trituberculatus. Population structure analysis, phylogenetic tree, and principal component analysis (PCA) demonstrated that the seven groups ofP. trituberculatuswere divided into four subpopulations (K = 4), but the correlation between genetic structure and geographical distribution was not obvious. These results are expected to provide useful information for the fishery management of wild swimming crabs.