Abstract: 【Objective】 In order to understand the genetic diversity and generational genetic differentiation of breeding populations of red shell color Meretrix meretrix during population selection,and to provide theoretical basis for long-term sustainability of breeding programs.【Method】 In this study,fifteen pairs of microsatellite markers were used to analyze seven populations of M. meretrix,including Jiangsu wild population with yellow shell(SY),wild population with red shell(SR)and five generations selected consecutively though red shell and shell length(SRF1-SR5F5). Fifteen pairs of microsatellite primers were used for PCR amplification of genomic DNA of sevenpopulations. The genetic diversity of seven populations was analyzed by online softwares such as Gel-Pro32 4.0,PopGen 32 and MEGA 6.0.【Result】 The results showed that a total of 766 alleles were detected in seven populations, and 3 to 18 alleles were detected at each microsatellite locus in each population. The number of alleles(Na)decreased with the increase of breeding generations. The mean polymorphic information content(PIC)of the 15 microsatellite loci ranged from 0.575 to 0.630,so they were highly polymorphic loci. The average observed heterozygosity(Ho)and expected heterozygosity(He)were 0.442-0.502 and 0.629-0.680,respectively. 63.81% of microsatellite loci deviated from Hardy-Weinberg equilibrium,indicating a certain degree of heterozygous deletion at each microsatellite locus. The number of inbreeding lines(F_is)ranged from -0.0157 to 0.7409,with an average of 0.2777,indicating that there was a certain level of inbreeding in the population. The average coefficient of genetic differentiation(F_st)between populations was 0.0455,that was,4.55% of the population variation was caused by gene differences between different populations,and 95.45% of the population variation was from within populations. The gene flow(Nm)of each population ranged from 0.9002 to 18.9478,with an average of 8.8065,indicating low genetic differentiation among the seven populations. UPMGA cluster analysis showed that the seven clam populations clustered into two branches,the SR and its breeding population clustered into one branch,and SY clustered into one branch.【Conclusion】 After five generations of artificial selective breeding,the genetic diversity index of the selected population decreased slightly compared with SR and SY,but the genetic structure of the selected population did not change andthey still had a high genetic diversity. In the continuous selective breeding program,the breeding environment of parents should be diversified to avoid the genetic drift or inbreeding decline caused by the small size of artificially bred parents and breeding population,which leads to the deletion of some alleles in breeding population and the change of genetic structure of offspring.