A member of growth factor and a member of the transforming growth factor β superfamily, growth differentiation factor 9 (GDF9) has a critical role in prolificacy of sheep and goat. In this study, we analyzed exon 1 of the GDF9 gene in Indonesian goats. For this purpose, 77 blood samples representing nine Indonesian goat breeds (Gembrong, Senduro, Ettawa Grade, Boerawa, Boerka, Kosta, Samosir, Boer, and Kacang) were collected. An exonic region of GDF9 gene, 462 bp in length, was amplified using specific primers. Two single nucleotide polymorphisms (SNPs); SNP g.306G>A and SNP g.228C>A, were identified based on reference and direct sequencing, respectively. SNP g.306G>A was used to genotype all animals using RFLP method with HhaI restriction enzyme. The results revealed an absence of polymorphism of GDF9 gene at SNP g.306G>A in all animals investigated. Further study on SNP g. 228C>A showed polymorphism of GDF9 gene in all Indonesia goats except Senduro, Ettawa Grade, Boerawa and Samosir goats. In average, the frequency of C allele (88%) is higher than A allele (12%), followed by CC (77%) and CA (23%) genotypes. However, in Boer goat, the CA genotype (75%) is higher than CC genotype (25%). These population was not deviated from Hardy Weinberg Equilibrium (P>0.05) based on SNP g.228C>A. In conclusion, SNP g.228C>A might be suggested as a tool for Indonesian goat marker selection based on the gene encoding prolificacy trait.