Abstract: Galaxea fascicularis is a representative species of reef-building coral in the South China Sea. Based on the nematocyst morphology and the indel genotype of CYTB-ND2 in mitochondrial genome, G. fascicularis can be divided into two morphotypes: S and H, and there is significant differentiation in the genetic and ecological phenotypes between these two morphotypes. By mining microsatellite resources from the transcriptome sequences, we developed 11 SSR markers that could be used in both morphotypes, and tested and validated them in one S population （n = 16） and one H population （n = 31）, respectively. All the 11 markers showed polymorphism. In S population, the number of alleles ranged from 3 to 8 （mean 4.8±1.9）, the observed heterozygosity （H_O） ranged from 0.06 to 0.92 （0.55±0.26）, and the expected heterozygosity （H_E） ranged from 0.24 to 0.83 （0.40±0.27）. In H population, the number of alleles were 2～9 （4.5±2.1）, the observed heterozygosity （H_O） was 0.17～1.00 （0.70±0.15）, and the expected heterozygosity （H_E） was 0.46～0.86 （0.62±0.19）. Only one locus （Gf-E24） deviated from the Hardy-Weinberg equilibrium in H population, probably due to the presence of null allele.