Alosa sapidissima has emerged as a newly imported premium fish species with high value in promoting large-scale aquaculture in China in recent years. Understanding the genetic background of cultured and wild populations of A. sapidissima is crucial for evaluating germplasm resources and breeding new strains. In this study， 20 polymorphic simple sequence repeats （SSRs） were selected to evaluate the genetic diversity and genetic structure of 3 cultured populations and 2 wild populations of A. sapidissima. A total of 201 alleles were detected from 20 polymorphic microsatellite markers average of 10.05 alleles per marker. Among the five populations， the average of the effective alleles （N_e）， the observed heterozygosity （H_O）， expected heterozygosity （H_e） and polymorphism information content （PIC） ranged from 2.675 4 to 4.136 0， from 0.675 0 to 0.775 0， from 0.601 8 to 0.729 8 and from 0.547 3 to 0.698 8， respectively. The analysis of molecular variance （AMOVA） indicated that the genetic variance within individuals accounts for 94.93% and the genetic variance among populations accounts for 5.07%. The result of genetic differentiation index （F_st） analysis showed that the YSF₁ had a moderate level of genetic differentiation from the YZF₄ and YZF₅ （0.05<F_st<0.15）， and the genetic differentiation of the other pairwise populations was weak （F_st<0.05）. The result of the Hardy-Weinberg equilibrium showed that 31% of group loci were found to deviate significantly from the Hardy-Weinberg equilibrium after sequential Bonferroni correction （P<0.05）. The UPGMA cluster tree based on the Nei's genetic distance showed that five populations were divided into two branches and the similar result also obtained from PCoA analysis and Bayesian Structure clustering analysis. Results indicated that the cultured populations of A.sapidissima introduced into Shanghai retain a relatively high level of genetic variation and hold significant genetic breeding potentiality.