Abstract: By mining the EST and genomic microsatellite sequence resources of Porites species in GenBank, and using interspecific amplification and resequencing, we developed the microsatellite markers for Porites lutea symbiont, and by identifying with pure zooxanthella DNA, 20 P. lutea microsatellite markers and 43 microsatellite markers of its symbiotic zooxanthella were validated. These markers of P. lutea were genotyped in one wild population（n=16） in the southwest of Hainan Island fringing reef. Nineteen of the 20 markers showed polymorphism.The number of alleles was 2～7（mean 3.5±1.8）, and the observed heterozygosity（H_o） and expected heterozygosity（H_e） were 0.06～0.94（mean 0.34±0.29） and 0.18～0.83（mean 0.57±0.20）, respectively. Four markers remained deviated from the Hardy-Weinberg Equilibrium（HWE） after multiple comparison correction for Bonferroin(P_HWE＜0.05), probably due to the presence of null alleles. This is the first set of microsatellite markers for P. lutea. They should be useful for the research on the genetic diversity and connectivity of this species and the conservation of endangered coral reef ecosystems and reef-building coral communities in the Indo-Pacific region.