The bighead carp (Hypophthalmichthys nobilis) is a native freshwater fish species in China. However, the wild fishery resources of H. nobilis have recently suffered a drastic decline. In this study, a total of 106,657 putative SNP loci were identified from the assembled transcripts of H. nobilis. Thirty-seven polymorphic loci were characterized from 60 SNP loci randomly selected for validation by using 36 fin clips of H. nobilis from the Yangtze River. The observed heterozygosity, expected heterozygosity, and polymorphic information content of the 37 SNP loci ranged from 0.171 to 1.000, 0.159 to 0.509, and 0.144 to 0.375, respectively, and 13 SNP loci significantly deviated from the Hardy–Weinberg equilibrium (P < 0.01). The SNP loci identified and validated in this study will be useful for the genetic research of H. nobilis.