The bay scallop (Argopecten irradians) is a simultaneous hermaphroditic marine bivalve with distinct male and female gonads, and external fertilization.crossbred, inbred and selfed families standing for the different inbreeding level could be produced.In this study, we selected 10 microsatellites to check the segregating distortion in two crossbred, two inbred and four selfed families (3 selfing for one generation and 1 for two generation).The crossbred families were found to have the most number of segregated markers, then were the selfed families for one generation and the selfed families for two generations, and the inbred families were found to have the least number of segregated markers.The homozygote deficiency was only found in the selfed families and the three markers might be linked to the lethal genes.we also found that the homozygous rate of the two growth related loci is lower.