The genetic diversity and relationship among South and East Asian melon Cucumis melo L. were studied by using RAPD analysis of 69 accessions of melon from India, Myanmar, China, Korea, and Japan. The genetic diversity was large in India, and quite small in Group Conomon var. makuwa and var. conomon from East Asia, clearly indicating a decrease in genetic variation from India toward the east. Cluster analysis based on genetic distance classified 17 groups of accessions into two major clusters: cluster I comprising 12 groups of accessions from India and Myanmar and cluster II that included five groups of accessions of Group Conomon var. makuwa and var. conomon from East Asia. Cluster I was further divided into three subclusters, of which subclusters Ib and Ic included small- and large-seed type populations, respectively. Therefore, this division was based on their seed size, not cultivation area. The large-seed type from east India was differently included in the subcluster of small-seed type (Ib). A total of 122 plants of 69 accessions were classified into three major clusters and subclusters: clusters I and II comprised melon accessions mostly from India and Myanmar, and cluster III comprised Group Conomon var. makuwa and var. conomon from East Asia. The frequency of large- and small-seed types was different between clusters I and II, also indicating genetic differentiation between large- and small-seed types. One plant of the small-seed type from east India was differently included in cluster III, and two plants from east India were classified into subcluster IV. These results clearly showed that South Asian melon is genetically differentiated by their seed size, and that small-seed type melon in east India is closely related to Group Conomon var. makuwa and var. conomon.