Abstract: Artificial reefs play an important role in improving the hydrodynamics of sea bottom, ensuring shelter, fish attraction/production, as well as stepping stones for marine species. In this paper, we selected 10 pairs of microsatellite primers to evaluate the effect of artificial reefs on genetic diversity and biological connectivity of Charybdis japonica in Juehua Island, Bohai Sea. The Charybdis japonica samples were from five communities of seagrass-beds, two natural reefs, sand sediments, and artificial reefs ecosystem. The results showed that the effective alleles N_e of the 10 loci ranged from 4.82 to 17.72, and the observed heterozygosity H_o and expected heterozygosity H_e were 0.30 to 0.76 and 0.67 to 0.95, respectively. The genetic diversity in Charybdis japonica from various ecosystems was at a high level, in which with effective allele number N_e ranged from 6.03 to 7.45, observed heterozygosity H_o ranged from 0.64 to 0.74, expected heterozygosity H_e ranging from 0.85 to 0.88. The mean Shannon information index is about 1.95±0.07, and polymorphism information content PIC from all ecosystems was 80.03±1.31%. The average F-statistics (F_IS, F_IT, F_ST) of 10 microsatellite loci of Charybdis japonica were 0.207±0.156, 0.240±0.152, and 0.050±0.013, respectively, which indicated the different inbreeding degree of genetic differentiation. The FIS values of the Charybdis japonica genetic differentiation among various ecosystems ranged from 0.001 to 0.026, and the genetic differentiation in Charybdis japonica of all the paired ecosystems was small (F_IS <0.05). The gene flow of Charybdis japonica ranged from 9.410 to 567.932, all of which were greater than 1. The level of gene exchange in Charybdis japonica among different ecosystems was high, showing a strong biological connectivity. The biological connectivity among seagrass-beds, natural reefs and artificial reefs is extremely high, while that of the sand sediment with other ecosystems were low. The results verified that artificial reefs have beneficial effects to habitat restoration and resource conservation.