Hucho bleekeri, also called Sichuan taimen, is a species endemic to Yangtze River drainage in China. Due to habitat destruction, heavy fishing and pollution, the wild population of H. bleekeri has declined rapidly in recent years. Insufficient molecular markers have limited the effective conservation of this species. In the present study, 34 novel single nucleotide polymorphism (SNP) markers were developed in H. bleekeri based on restriction site-associated DNA sequencing (RAD-seq). The minor allele frequency ranged from 0.059 to 0.486, and the observed and expected heterozygosities ranged from 0.118 to 0.861 and 0.112 to 0.507, respectively. Polymorphic information content ranged from 0.105 to 0.375. Among these SNPs, four loci showed significant departures from the Hardy–Weinberg equilibrium (P < 0.01). The novel polymorphic SNPs will be useful for future investigation of population structure and conservation genetics for this species.