Eight polymorphic microsatellite loci were isolated and characterized from the orange-fin anemonefish (Amphiprion chrysopterus). These loci provided markers with polymorphisms of 4–14 alleles per locus within 151 individuals from Moorea, French Polynesia. The expected heterozygosities ranged from 0.53 to 0.88. High variability suggests that these markers should be useful to study paternity, population structure, and connectivity in this species.