Abstract: Artificial reefs improve the hydrodynamics at sea bottom, providing shelter and stepping stones for marine species, and facilitate fish attraction/production． In this work, 10 pairs of microsatellite primers were selected to evaluate the effect of artificial reefs on genetic diversity and biological connectivity of Charybdis japonica in Juehua Island, Bohai Sea． Charybdis japonica samples were taken from five communities of seagrass-beds, two natural reefs, sand sediments, and artificial reefs ecosystem． The effective alleles N_e of the 10 loci was 2.94-17.72, the observed heterozygosity H_o and expected heterozygosity H_e were 0.30-0.82 and 0.67-0.95, respectively． Genetic diversity of Charybdis japonica from various ecosystems was high, the effective allele number N_e was 6.06-7.45, observed heterozygosity H_o ranged from 0.64 to 0.74, expected heterozygosity H_e was from 0.85 to 0.88． The mean Shannon information index was 1.95 ± 0.07, and polymorphism information content PIC from all ecosystems was (80.03 ± 1.31)%． Average F-statistics (F_IS, F_IT, F_ST) of the 10 microsatellite loci of Charybdis japonica were 0.207 ± 0.156, 0.240 ± 0.152, and 0.050 ± 0.013, respectively, indicating different inbreeding degree of genetic differentiation． F_ST values of Charybdis japonica among various ecosystems ranged from 0.001 to 0.026, the genetic differentiation in Charybdis japonica of all the paired ecosystems was small (F_ST < 0.05)． The gene flow of Charybdis japonica was from 9.410 to 567.932, much greater than 1． The level of gene exchange in Charybdis japonica among different ecosystems was high, showing strong biological connectivity． The biological connectivity among seagrass-beds, natural reefs and artificial reefs was very high, but that of the sand sediment with other ecosystems was low． This verified that artificial reefs have beneficial effects for habitat restoration and resource conservation．