Forty polymorphic microsatellite loci were developed from Crassostrea hongkongensis using an enriched partial genomic library with magnetic beads. The polymorphism of these loci was assessed in 30 individuals from a wild population. The allele number of the polymorphic markers ranged from 2 to 13, with an average of 5.8 per locus. The polymorphism information content ranged from 0.032 to 0.891 and 37 loci presented a medium or high level of polymorphism. The observed and expected heterozygosity values ranged from 0.033 to 1.000 and 0.033 to 0.931, respectively.