Nine microsatellite loci were isolated and characterized in the tire track eel, Mastacembelus favusby using library enriched for microsatellite region. Among 47 specimens collected from Mekong River, the number of alleles ranged from 2 to 17 while levels of observed and expected heterozygosities ranged from 0.021 to 0.873 and from 0.021 to 0.893, respectively. The primers were successfully tested in six closely related species, hence valuable for investigating population genetics and other related aspects of M. favus and its congener species.