Abstract: Schizothorax dolichonem is an endemic fish species that mainly distributes in main streams and tributaries of the upper reaches of the Yangtze River in China. In the Yanglong River basin, S. dolichonem is one of the main catch objects, playing an important role in fishery production of Yanglong River. In recent years, many factors such as pollution, overfishing, damming, habitat degradation and environmental change, have seriously affect its natural resources, especially the cascade hydropower development in the middle and lower reaches of Yalong River. Fragmentation caused by hydropower stations may disrupt communication of fish populations and influence population genetic structure and diversity. A good understanding of population genetic structure would be useful for better conserving and restoring the natural resources of this schizothoracin. In present study, 118 individuals of S. dolichonem sampled from Ganzi, Yangjiang, Jinping and Jinhe sections of Yanglong River in the year 2018 were analyzed, using the complete mitochondrial cytochrome b gene sequences. The result showed that the length of Cyt b gene of was approximate 1085 bp. 19 haplotypes and 29 polymorphic sites were found among 118 S. dolichonem individuals. The total haplotype diversities (Hd) and nucleotide diversities (π) were 0.850 ± 0.017 and 0.003 35 ± 0.001 89, respectively. The Hd ranged from 0.697 ± 0.069 to 0.831 ± 0.022, and π from 0.000 92 ± 0.000 79 to 0.006 22 ± 0.003 36 among the four groups, respectively. Analysis of molecular variance (AMOVA) showed that most of the genetic variation occurred within groups (84.84%). The neutrality test and mismatch distribution indicated that the population of S. dolichonem in the Yanglong River had experienced an expansion. Pairwise fixation index (FST) values indicated significant differentiation between any two groups (FST ranged between 0.090 48 - 0.199 17, P < 0.05), except between Ganzi and Yangjiang groups (FST = 0.043 47, P > 0.05). Although significant FST values were found among geographical groups, the differentiation level still belonged to intra-population differentiation, suggested that these groups of S. dolichonem in Yanglong River should be considered as a single management unit. In conclusion, this study provided valuable information for restoration of S. dolichonem natural resources in Yanglong River and theoretic knowledge for a rational utilization of the germplasm resources.