Liobagrus angullicauda is an endemic species to streams along the southeast coast in China. Due to over fishing and habitat destruction, the natural population of L. angullicauda has decreased dramatically in recent years. Insufficient molecular markers have limited the effective conservation and management of this species. In the present study, we reported the isolation and characterization of 33 SNP markers in L. angullicauda. The minor allele frequency ranged from 0.083 to 0.507, and the observed and expected heterozygosities ranged from 0.177 to 0.624 and 0.290 to 0.712, respectively. Polymorphic information content ranged from 0.118 to 0.408. Among these SNPs, only four loci showed significant departures from the Hardy–Weinberg equilibrium (P < 0.05). Cross-amplification was tested in related species Liobagrus nigricauda, Liobagrus marginalus and Liobagrus marginatoides. The novel polymorphic SNPs should be helpful for the future study on genetic management and population conservation for this species.