Melon is a very important economically horticultural crop around the world. At present, andromonoecy is a widespread sexual system in traditional cultivar melon carrying both male and bisexual flowers, and andromonoecious maternal lines necessitate laborious hand emasculation for F1 hybrid seed production. Thus, gynoecious without emasculation will save labor cost and greatly?improve?the efficiency?of?hybrid?seed production, with?significant mean on improving the purity of hybrid seeds. Gynoecious melon plants are commonly genotypically designated as AAgg, and the phenotype-dependent selection of g recessive allele for breeding new gynoecious is slow and time-consuming. To accelerate the breeding of elite gynoecious lines, development of molecular markers linked to g allele might greatly contribute to the molecular marker assisted selection breeding. In this study, an allele-specific maker for g gene, g-FR, was developed based on a Gyno-hAT transposon on downstream of CmWIP1 locus. The sex phenotype and genotype of 141 F2 plants derived from hermaphrodite B15 and andromonoecious 054 was co-segregated based g-FR analysis. And the result was verified by two tightly linked molecular marker C5-9 and C5-10, which suggested that the accuracy of genotypic analysis of g-FR almost reaches to 100.0% in F2 population. Furthermore, we tested this newly-developed marker in genotyping of thirty-six melon accessions, and identified two bisexual genotypes B15 and B18. Taken together, these results will greatly facilitate the utilization of g gene in melon gynoecious breeding programs by marker-assisted selection.