Abstract: 【Objective】Studying the population immune gene diversity and genetic structure could effectively assess the current status，and provide a theoretical basis for conservation and rational exploitation of the wild resources of Triplophysa pappenheimi.【Method】The genetic diversity and structure of the natural populations of T. pappenheimi，sampled from different reaches of the middle and upper reaches of the Yellow River，Xunhua（XH）and Datong（DT）in Qinghai Province，and Jingtai（JT）in Gansu Province，were analyzed by using the recombination activating gene 1（Rag1）sequences.【Result】Eight unique haplotypes（H1-H8） were identified in Rag1 sequence from all individuals of T. pappenheimi. Five haplotypes（H1，H2，H3，H4 and H6）shared between any two of populations，and three of them（H1，H4 and H6）shared among all populations. The haplotype and nucleotide diversities of T. pappenheimi were 0.742 and 0.003， respectively. Twenty eight polymorphic sites were detected in three populations. Haplotype diversity ranged from 0.575 to 0.872 and nucleotide diversity ranged from 0.002 to 0.003 among populations. The genetic differentiation coefficient（Fst） value between XH and JT，between XH and DT，and between JT and DT were 0.037，-0.041，and -0.022，respectively. The molecular variation analysis（AMOVA）revealed high genetic variation within populations（99.56%）. Both NJ and ML phylogenetic tree and haplotype network analysis showed that individuals from different populations were mixed together and did not form obvious cluster according to phylogeographic structure. Mixed distribution patterns were presen ted between the different haplotypes in T. pappenheimi.【Conclusion】It is suggested that these natural populations of T. pappenheimi have the middle level of genetic diversity. Different levels of genetic diversity are found among these wild populations. Moreover，it is not obviously identified genetic divergence among the populations of T. pappenheimi. It is suggested that management and conservation of these populations in the field can be regarded as a whole.