Twelve individuals from the allotetraploid crucian-carp,common carp, and red crucian carp were analyzed by using 32 pairs microsatellite primers of the poly (CA) type which were isolated from common carp (Cyprinus carpio L.) by Crooijmans et al. Electrophoretogram patterns showed that 15 pairs of microsatellite primers reproducibly produced the well-identifiable bands. The number of alleles per marker varied from 1 to 8, and the size of alleles ranged from 100 bp to 420 bp. The genetic similarity index between the allotetraploid crucian-carp and their original maternal red crucian carp was 0.5625, and the genetic similarity index between the allotetraploid crucian-carp and their original paternal common carp was 0.5125. The similarity index between red crucian carp and common carp was 0.4204. Both microsatellite and RAPD showed the similar results of the genetic similarity index. However, greater genetic distances were found among microsatellite markers than those among RAPD. These results demonstrate that the microsatellite-based analysis of the genetic variation is useful in measuring intrabiotype differences.