Shelf-life of fruit is one of the most important traits in melon breeding. Shelf-life of climacteric fruits is closely related with ethylene whose biosynthesis is controlled by ACC synthase and ACC oxidase genes. As the first step to develop selection markers for shelf-life in melon (Cucumis melo), microsatellite and cleaved amplified polymorphic sequence (CAPS) polymorphisms were analyzed in two ACC synthase genes (CMe-ACS1, CMe-ACS2) and two ACC oxidase genes (CMe-ACO1, CMe-ACO3), resulting in the establishment of six microsatellite and two CAPS markers. Five markers were developed in two genes, CMe-ACS1 and CMe-ACO1, which were expressed during fruit ripening. A highly polymorphic marker was found in CMe-ACS2, where the number of simple sequence repeat of (TA) was highly variable among cultivars, ranging from seven to thirty-seven. Insertion/deletion of (T)n and (A)n was also detected in CMe-ACS2. CAPS and microsatellite markers specific to vars. makuwa and conomon, local varieties in East Asia, were detected in four markers, Acs1-c1, Acs2-ms1, Aco1-ms2 and Aco3-ms1, and could be useful markers for phylogenetic analysis in melon.