The mitochondrial cytochrome b gene fragments of eight cyprinoid aquaculture breeds were sequenced and their genetic diversity and cluster analysis were compared. Mean content of T, C, A, G, are 26.8﹪, 29﹪, 29.7﹪, 14.5﹪, respectively, and A plus T is higher than G plus C. The mutations in the 141 amino acids translated by 425bp of Cyt b gene fragment, could not affect its function dueing that the majority were generated between the valin and isoleucine which were unchanged and hydrophobic. The result demonstrated that the evolution of this protein was slowly, and it was adapted for the genetic analysis. Five haplotypes were detected from 140 individuals, of which 75.5 percents belong to the Hap2, and the Hap1 was mainly distributed in the mirror carp. The AMOVA and cluster analysis based on Kimura 2-parameter model exhibited very close relationship among Germany mirror carp, Scattered mirror carp, Red mirror carp, and also revealed that the relationship among Cyprinus carpio blue var, Cold-resistance strain of red purse carp, Frigid carp was close. The results were in accordance with their breeding backgrounds.