The Taipei grass frog, Hylarana taipehensis, is a slender frog widely distributed throughout Southeast Asia and thus is predicted to contain a high level of genetic diversity and undetected endemics. Habitat destruction and pesticide pollution have resulted in the population crash of some genetically distinct populations. To assign appropriate conservation measures, a genetic survey covering individuals from the entire species’ range is urgently required to reveal cryptic diversity and delineate these frogs into various management units. However, effective codominant markers are lacking for this species. Here, we reported 22 tetranucleotide microsatellite loci for H. taipehensis. Alleles ranged between 6 and 17 per locus. The observed heterozygosities and expected heterozygosities were 0.280-0.893 and 0.721-0.908, respectively. These polymorphic microsatellites should be useful in identifying the most important units for conservation management of the Taipei grass frogs.