Using microsatellite markers we determined polymorphism of genomic DNA and classification in four important cultivation species: Common carp ( Cyprinus carpio haematopterus
Temminck et Schlegel), Scatter scaled mirror carp (C. carpio
), Frigid-resistant strain of Purse red carp ( Cyprinus carpio
) and Songpu carp (C. carpio
Songpu carp). Amplifications with 24 pairs of primers gave a total of 3 882 fragments ranging from 126 bp to 489 bp in the 4 populations, which included 12 pairs of microsatellites designed according to zebrafish function gene sequences and 12 pairs of microsatellites isolated from common carp. 1-5 alleles per locus in 4 species were amplified, and there were 59 alleles in all populations except common carp which had only 21 loci and 55 alleles. The average number of alleles was 2.46. Additionally, a clustering analysis was made based on the results of the PHYLIP software package (version 3.6) and phylogenetic trees were constructed by MEGA3. The bootstrap values were evaluated for each crunode of the dendrogram by means of 1 000 reiterations of the bootstrap test using the Maximum Likelihood method, the Neighbor-Joining method and the UPGMA method. With these methods we made three observations. (1) the level of genetic variability is relatively high in all populations. Observing value of mean heterozygosity varies from 36.43% to 43.79% and expected value of mean heterozygosity varies from 49.49% to 53.29%. All populations show significant heterozygote deficiencies. (2) The genetic similarity indexes are all above 0.84, indicating closeness of their genetic relationship. The genetic distances are small, ranging from 0.067-0.170. The phylogenetic tree shows that Songpu carp and Scatter scaled mirror carp are the nearest in relationship and Frigid-resistant strain of Purse red carp is better correlated with them than the Common carp. (3) There is no aim fragment amplified in 3 loci of zebrafish function gene microsatellites in the population of common carp, which may mean that the flanking sequence of the microsatellites have changed while the PCR primers were designed according to them or the genomes of common carp have lost these function genes or loci. More research is needed to explore the physiological mechanism and biochemical process. In conclusion, these 24 microsatellite markers can be used for the evaluation of genetic diversity in carps. Three microsatellite markers reveal polymorphism between the common carp and the other three carps, and can be used to distinguish them.