Fenneropenaeus penicillatus, with high protein and low fat, is a commercially important aquatic product in China. Microsatellite loci were developed according to the protocol of fast isolation by amplified fragment length polymorphism of sequences containing repeats. Eight new polymorphic microsatellite markers for F. penicillatus were identified, and 32 wild individuals were used to evaluate the degree of polymorphism of these markers. The polymorphism information content ranged from 0.2703 to 0.7598, and the number of alleles per locus varied from 3 to 6. The observed and expected heterozygosities were 0.1613-0.5556 and 0.2347-0.7387, respectively. No significant deviations from Hardy-Weinberg equilibrium (P > 0.00625) were detected. These polymorphic microsatellite loci will be useful to study the genetic diversity and population structure of F. penicillatus.