Abstract: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 InDelOr1. 28 melon accessions were genotyped using this marker, and results showed that the polymorphism of InDelOr1 marker was cosegregated with the flesh color, allowing us to identify the homozygous orange flesh genotype, homozygous nonorange 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 IndelOr1 marker. The accuracy of genotyping results reached 97.4% and 95.3% respectively in two populations. The results showed that IndelOr1 marker had high accurate and the application promotion value, which could abundantly raise the efficiency of breeding and shorten the breeding cycle.