The genetic diversity of mtDNA Dloop in the population of Onychostoma rara from the Xijiang River, the Pearl River system was studied for the first time on the basis of determination of about 467 bp sequences of mtDNA Dloop in 30 individuals by the methods of PCR and DNA sequencing. The results showed that the length of the determined sequence in 30 individuals varied from 467 to 470 bp. A total of 16 variable loci (3.40% of total loci) were detected in the sequence of mtDNA Dloop in the population, and the total percentage of bases A and T (67.6%) was much higher than that of bases C and G (32.3%) in the sequence. The mtDNA Dloop of Onychostoma rara comprised the termination associated sequence domain, the central conserved sequence domain and the conserved sequence block domain, and the extended termination associated sequence (ETAS), 3 conserved blocks (CSB-F,CSB-E,CSB-D) in the central conserved sequence domain and 1 conserved sequence blocks (CSB1) in the conserved sequence block domain were successfully identified in the population. The 30 individuals belonged to 11 haplotypes according to the determined sequences. The haplotype diversity (H_d) was 0.733 3, and the average genetic distance (P) between the haplotypes of the population was 0.010 2. The nucleotide diversity (P_i) of the 30 individuals was 0.005 79, and the average number of nucleotide differences (K) of them was 2.705 75.The UPGMA phylogenetic tree of the 11 haplotypes comprised 2 branches. The population of O. rara from the Xijiang River possessed abundant genetic diversity.