Orange flesh is one of the most important trait in current melon breeding. According to the alignment between the nucleotide sequences of CmOr in orange versus green/white flesh fruit, we captured an insert/deletion mutation and developed an InDel marker named InDelOr1. 28 melon accessions were genotyped using this marker, and results showed that the polymorphism of InDelOr1 marker was cosegregated with the flesh color, allowing us to identify the homozygous orange flesh genotype, homozygous nonorange flesh genotype and heterozygous orange flesh genotype. Two F₂ populations were constructed from the hybrid combinations between melon accessions with white flesh and orange flesh, which were then genotyped by IndelOr1 marker. The accuracy of genotyping results reached 97.4% and 95.3% respectively in two populations. The results showed that IndelOr1 marker had high accurate and the application promotion value, which could abundantly raise the efficiency of breeding and shorten the breeding cycle.