The starfish (Asterina pectinifera) is a common species widely distributed along the coasts of East Asia. Nevertheless, little information is currently available about the genetic characteristics of native populations. In this survey, the first set of 14 microsatellite markers for the starfish was developed from expressed sequence tag databases. They were characterized using 40 samples. Number of alleles per locus ranged from three to 14. The observed and expected heterozygosities ranged from 0.300 to 0.825 and from 0.479 to 0.919, respectively. These informative microsatellite markers will be useful in studies of population genetic structure for this species.