Abstract: Anabarilius graham is a kind of native fish in the Fuxian Lake, Yunnan Province, and its germplasm resources had been drastically reduced since the 1990s due to overfishing and invasive species. After many years of artificial propagation and releasing, in order to realize the present genetic diversity, we sampled a total of 133 Anabarilius graham from 7 geographic populations and conducted genetic diversity analysis based on sequences of D-loop control region. The results showed that A+T base composition (62.28%) was higher than the C+G combination (37.72%); A total of 40 polymorphic sites were identified and 36 haplotypes were defined. The overall haplotype diversity index (H_d) was 0.791±0.036 and the overall nucleic acid diversity index (π) was 0.00254±0.00027, which suggested a distribution of “high H_d and low π”. The average H_d and π of west group (H_d=0.826—0.846, π=0.00236—0.0031) was higher than that of east group (H_d=0.657—0.805, π=0.00204—0.00271). The highest and lowest index value of nucleic acid diversity and haplotype diversity were identified in MX and XB population, respectively. What’s more, the furthest genetic distance was found between LQ and HJ population, but insignificant genetic differentiations were identified in 7 populations. The results of the neutrality test (Tajima’s D=–1.73617, P=0.03729; Fu’s F_s=–1.64259, P=0.23943) and nucleotide mismatch distribution revealed that no population expansion happened in evolutionary history of Anabarilius graham. In conclusion, the distribution of “high H_d and low π” was identified in Anabarilius graham, which could be caused by faster evolutionary speed in mitochondrion. Meanwhile, insignificant genetic differentiations among each population may be caused by the dispersive life history of Anabarilius graham and artificial releasing. This study preliminarily revealed the current genetic diversity of Anabarilius graham in the Fuxian Lake, and provided necessary basis for the protection of germplasm resources and genetic breeding.