The nuclear DNA of two populations of Andrias davidianus was amplified by PCR. The amplified fragments including 5.8S and 28S nuclear ribosomal RNA gene partial sequence and the nuclear ribosomal second internal transcribed spacer (ITS2) complete sequence. The length of the fragment contained 606 bp nucleotides. The genetic diversities of Andrias davidianus from the Changshou Lake Rare Fish Breeding Center (CSLRFBC) of the Chongqing Fisheries Research Institute and Guanghan Rare Aquaculture Company (GHRAC) were analyzed. The result indicated as follows. The T, C, A and G average contents were 15.6%, 36.5%, 12.5% and 35.4% respectively. The average contents of G+C and A+T were 71.9% and 28.1% respectively. The average values of transversional pairs were 271 and transitional pairs were 112. The ratio of transition and transversion was 0.41, and the ratio of transversion exceeded that of transition significantly. The 10 individuals belonged to 10 haplotypes according to the determined sequences. The haplotypic diversity (H) was 1.0000±0.1260, and the average number of nucleotide differences (K) of them was 5.9321±0.8614. The nucleotide diversity (Pi) of the 10 individuals was 0.6319±0.0139. The correlation within populations relative to total was 0.0305 to the two populations. Two populations have not differentiated to a single population by test of Tajima^,s D, Fu＆Li^,s D, F and cluster analysis.