Abstract: To assess the genetic diversity of cultured rock carp Procypris rabaudi from Changshou and Fulin districts in Chongqing city, partial DNA sequences of mtDNA control region (D-loop) were amplified from 175 individuals by PCR. A total of eleven haplotypes were determined by sequence alignments of the amplified 692 bp sequences. Among them, Hap1 was the main haplotype, accounting for 76.57% of the entire individuals. The haplotype of Hap10 possessed the highest evolutionary rate, and shared the farthest evolutionary distance with Hap6. The haplotype diversities of cultured P. rabaudi from Changshou and Fulin districts were 0.4100±0.0550 and 0.3970±0.0820, respectively, and their nucleotide diversities were 0.0013±0.0003 and 0.0013±0.0004, respectively. The genetic diversities were compared with wild populations from the upper Yangtze River drainage (including reaches of Cangxi, Hejiang, Wanzhou, Wulong, Xishui and Tanghe), and cultured population from Beibei district. The results indicated that the genetic diversity of cultured P. rabaudi from Changshou and Fulin districts was obviously lower than that of wild populations, but slightly higher than that of cultured population from Beibei district. To sustain the genetic diversity of cultured rock carp, it is necessary to choose parent fish with further genetic distances for propagation, and to supplement new broodstocks with different genetic background as well.