The sea urchin Strongylocentrotus intermedius was originally found off the coast from Hokkaido, Japan and Far East Russia and was introduced from Japan to China in 1989. Now, is one of the most commercially important cultured sea urchin species in China. Family selection and individual selection have been used to genetically improve its economic traits. In order to clarify the genetic diversity and genetic structure of different breeding populations of S. intermedius, the genetic diversity and genetic structure of a family selection population (FP), an individual selection population, and a unselected common population (CP) were analyzed using SSR-seq technology and 15 microsatellite loci. The results showed that a total of 112 alleles were detected at 15 microsatellite loci, and the average number of alleles (N_a) observed in FP, IP and CP were 5.077, 5.133 and 6.133, respectively, with mean effective alleles (N_e) of 2.816, 2.873 and 3.638, respectively. The mean observed heterozygosities (H_o) in FP, IP and CP were 0.522, 0.441 and 0.501, respectively, and the mean expected heterozygosities (H_e) were 0.595, 0.599 and 0.667, respectively. The mean polymorphic information contents (PIC) in FP, IP and CP were 0.546, 0.543 and 0.623, respectively. The difference between H_e and H_o in FP (0.073) was lower than that in IP (0.158) or CP (0.166). The mean fixation index (F) in FP (0.115) was also lower than that in IP (0.248) or CP (0.246). The coefficients of genetic differentiation (F_st) among the three populations ranged between 0.018 and 0.176, indicating a low-to-medium degree of genetic differentiation. The analysis of molecular variance (AMOVA) results showed that the genetic variation of the three populations mainly come from individuals. Both principal component analysis (PCoA) and clustering phylogenetic tree showed that the three populations were closely related, and the IP population had the highest degree of genetic differentiation. In summary, our results suggest that the three sea urchin populations have high genetic diversity, and multiple generations of family selection and individual selection did not reduce genetic diversity dramatically. Family selection is more beneficial in maintaining population heterozygosity and controlling inbreeding levels. This research can lay a foundation for the evaluation and development of germplasm resources of the sea urchin S. intermedius.