Abstract: 【Objective】 To clarify the genetic structure and diversity of Onychostoma lini population from the Duliu River in the Pearl River system, and explore the endangered mechanism, and provide reference for protection countermeasures of the species.【Method】 The genetic diversity of whole genome DNA in the 30 individuals of O. lini collected in the river in Sandu, Xinghua and Rongjiang of Guizhou was analyzed by the methods of AFLP using 8 selected primer pairs, the parameters for genetic diversity including total number of amplified locus, number of amplified polymorphic locus, Shannon's information index(I), Nei's gene diversity index(H), polymorphism information content(PIC), number of observed allele(Na), number of effective allele(Ne) and genetic distance(D_A) were calculated by PopGene32. 【Result】 A total of 699 amplification fragments comprising 69-500 bp respectively were amplified using the 8 primer pairs. On average, 87.38 sites were obtained for each primer combination amplification. Among the 699 amplification sites, 663 were polymorphic loci accounting for 94.85% of the total. The 699 amplified loci were distributed in 10 intervals of occurrence frequency of locus in the 30 individuals of O. lini from the Duliu River. Of them, the number of amplified locus changed slightly in interval of occurrence frequency of 30%-89% but those in intervals of occurrence frequency of 0%-9% and 90%-99% both occurred peak values. The values of I, H, PIC, Na and Ne in the population averaged 0.3490, 0.2206, 0.6404, 1.9464 and 1.3574, respectively. The D_A of the 30 individuals ranged from 0.2305 to 0.4440, with an average of 0.3304. The UPGMA phylogenetic tree of the population based on D_A showed that, the 30 individuals was clustered into 2 branches based on the genetic distance, 18 individuals was clustered into a branch and the rest 29 into another.【Conclusion】 The population of O. lini from the Duliu River contained high genetic diversity, but the effective population size had become small and some effective alleles had been lost in the population, and therefore O. lini might be an ecologically endangered species. It is necessary to take measures to protect the O. lini population in the Duliu River.