Genetic structure of five hard clam stocks were detected using nine pairs of SSR primers and six ISSR primers. The shell color of one population is red and their offspring are red or yellow, while another population is yellow and their offspring are yellow also. The PIC，observed and expected heterozygosity of five populations detected from SSR ranged from 0.643 0 to 0.704 9 , 0.745 5 to 0.794 6 and 0.717 5 to 0.752 0,respectively. The percentages of polymorphic loci detected from ISSR were from 92.11% to 97.37%. The highest Shannon Index from PR population was 0.503 3 and the lowest from RF1Y was 0.412 6. Both two markers showed high polymorphism. Compared with their parents’, the genetic structure of the three offspring populations didn’t change. The results of cluster from the two kinds of markers were the same: the red shell color parents and their offspring gathered together at first, while the yellow parents and offspring gather together, then those two sub branches clustered into one group. Overall, the genetic diversity of the parents and their offspring was very high, and compared to their parents’, the genetic structure of the offspring didn’t change. That is to say, those offspring could be used for artificial breeding as parents seccessively.