The Cucurbitaceae (Cucurbits) family has 825 species in 118 genera, predominantly distributed in tropical and subtropical regions. Major cucurbit crops including cucumber (Cucumis sativa), melon (Cucumis melo), watermelon (Citrullus lanatus), and squash/pumpkin (Cucumis pepo) are important in the human diet and the rural economy. In recent years, large amount of genome information has been analyzed and reported in major cucurbit crops, such as cucumber, melon, and watermelon. To construct high quality reference genome sequence of Korean melon (Chamoe), genomic and transcriptomic sequence data were generated from Korean native (Gotgam) and elite (SW3) Chamoe inbred line using Illumina HiSeq2000 platform. In case of genome analysis, 4,773 scaffolds covering 98% of Gotgam Chamoe were assembled through de novo genome assembly and reference-based assembly. Large number of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were detected between two inbred lines and these markers were used for construction of genetic maps and discrimination of cultivars or species. In addition, genome sequence of other Chamoe and melon including Chang Bougi, Sakata’s Sweet, Prescott Fond Blanc and Banana melon will be constructed by de novo genome analysis. Genetic markers of these will also be detected and used for marker-assisted breeding and further analysis to investigate major traits of Chamoe, fruit color and flesh color. In conclusion, the newly constructed reference genome will provide genome information for comparative genomics and breeding of other cucurbit crops.