Ten polymorphic microsatellites were isolated from the red-bellied yellow tail fusilier Caesio cuning, a reef-associated fish which occurs widely in the Indo-Pacific region. The species is exploited by both small-scale and commercial fisheries. Fifty individuals from six populations were genotyped using primers that reliably amplified 10 polymorphic loci. The number of alleles per locus ranged from three to 11. Observed heterozygosity (HO) and expected heterozygosity (HE) ranged between 0.400 to 0.880 and 0.337 to 0.843, respectively. These microsatellite loci may be used to study population structure, genetic diversity and connectivity of C. cuning in the range of its distribution.