Eighteen polymorphic microsatellite loci were isolated and characterized from the endangered Black-fronted Tern (Chlidonias albostriatus), a species endemic to New Zealand. The loci were initially tested on seven individuals spanning the entire breeding range and then for a larger dataset of 345 samples covering 30 colonies from throughout the species' range. The number of alleles per loci ranged from 4 to 24, and observed and expected heterozygosity ranged between 0.46 and 0.95 and 0.45 to 0.86, respectively. One locus showed significant heterozygote deficit and appears to be sex-linked. The similar annealing temperatures across loci and the wide fragment sizes allowed multiplex polymerase chain reaction and rapid multilocus genotyping. The microsatellite markers will be useful tools for further investigation into the genetic diversity, population structure and effective population size of this endangered species and for informing conservation management.