AFLP analysis of genetic diversity in the three populations of sea urchin Strongylocentrotus intermedius (IN), S. nudus (NU) and F1 progeny (IN×NU) was carried out in this paper. In total, 272 loci were amplified with 4 primer pairs, of which 269 were polymorphic and the percentage of polymorphic loci was 98.89%. The Shannon diversity index for S. intermedius, S. nudus, and their hybrid populations was 0.2331±0.1273, 0.2005±0.1385, and 0.2625±0.1067, respectively. The genetic similarity within populations was 0.6876±0.0523, 0.6501±0.0548, and 0.6552±0.0553, respectively. AMOVA analysis indicated that 25.39% of variance was among populations and 74.61% of variance was within populations. This suggested the rich genetic diversity level within populations. Although the hybrids can be classified into two types by apparent characters, they were clustered each other by UPGMA method according to their genetic distances.