The fluorescent amplified fragment length polymorphism (fAFLP) technique was applied to analyze the genetic variation of 4 F1 groups (SS，JJ，SJ，JS) produced from matings and crosses of Shandong stock and Jiangsu stock in Meretrix meretrix. A total of 255 AFLP loci amplified with three pairs of primers were obtained from 96 individuals. The percentage of polymorphic loci ranged from 91.98% to 96.02% of 4 groups and the overall polymorphic loci percentage reached 97.65%. The results of Nei’s gene diversity and Shannon’s information index showed that the level of genetic diversity from high to low was SJ> SS> JS>JJ and the degree of variation of two hybrid groups was greater than that of two mating groups. The analysis of fAFLP loci indicated the frequency of dominant gene of SJ and JS increased and the genetic structure of two hybrid groups was similar to their maternal parent’s. By analyzing genetic similarity between groups, it was found that the genetic similarity was 0.976 1 between JS and JJ, 0.945 0 between JS and SS. And the genetic similarity was 0.950 2 between SJ and SS, and 0.925 4 between SJ and JJ. It is obvious that the genetic similarity (0.907 5) between SJ and JS was the lowest. Phylogenetic tree based on the genetic distance of 4 groups with NJ method and UPGMA method showed that JS and JJ were clustered together firstly because of the nearest genetic relationship, and SJ and SS were also clustered together. But it is evident that the phylogenetic relationship between SJ and other groups was more distant. In conclusion, hybridization between different geographical populations in Meretrix meretrix is a dominant approach to increasing genetic diversity and variation degree; two hybrid groups in genetic structure were similar to their maternal parent; high level of genetic diversity and variation degree of SJ group perhaps have a direct relationship with its heterosis in growth.