We studied the genetic diversity and genetic relationship of 28 melon parent materials using 2bRAD genotyping by sequencing, to provide a scientific basis for molecular marker assisted breeding of melon. The results showed that: (1) there were 10 318 SNPs in 28 melon germplasms, the ratio of transitions to transversions in SNPs was 2.15, and the mean value of the genetic variation and genetic distance between different germplasms were 0.88 and 2.22, respectively, implying the high degree of genetic differentiation among these germplasms. (2) According to the characters of skin color, fruit reticulation and flesh color, the 28 melon germplasms were separately divided into 4 populations (containing white skin population, yellow skin population, cyan skin population, and green skin population), 3 populations (containing smooth skin population, thin reticulation population, and dense reticulation population) and 3 populations (containing white flesh population, orange flesh population, and green flesh population). (3) The phenotypic analysis result showed that the degree of genetic differentiation among the populations classified by the skin color was the highest, and the value of the genetic variation was between 0.05 and 0.19, indicating a moderate or above level of genetic differentiation among the four populations; a moderate level of genetic differentiation was observed between smooth skin population and dense reticulation population, while there was no significant genetic differentiation between smooth skin population and thin reticulation population or between thin reticulation population and dense reticulation population; a moderate level of genetic differentiation was observed between white flesh population and orange flesh population, while there was no significant genetic differentiation between white flesh population and green flesh population or between orange flesh population and green flesh population. (4) These melon germplasms were divided into three subgroups by analysis of the phylogenetic tree. Specifically, the first subgroup had 11 germplasms (the parental germplasms were mainly selfselected melon varieties), the second subgroup had 9 germplasms (most of the parental germplasms were introduced from Xinjiang or selected from Xinjiang melon varieties), and the third subgroup had 8 germplasms (most of the parental germplasms were introduced from Japan or selected from Japanese melon varieties). The results of this study indicated that the clustering result of melon based on the molecular level exhibited a certain relationship with that of geographical origin, but it was not completely consistent with the result of the breeders classification about the breeding materials basing on skin color, fruit reticulation and flesh color.