Genetic structure and phylogenetic relationship among East and South Asian melons were analyzed, based on geographical variation of molecular markers. The analysis of Indian melon accessions exhibited a continuous variation in seed length, ranging from 4 to 13mm. Most of East Asian melon, vars. makuwa and conomon, were classified as small seed type whose seed length was shorter than 9mm. The frequency of small seed type increased from the west to the east in India. Gene diversity calculated for nine isozyme loci indicated that Indian melon was rich in genetic variation which decreased from India toward east. Clear geographical variation was detected in two enzymes, APS and 6-PGDH. Pgd-11 and Ap-31 were frequent in India and Myanmar, while most of the melons in Laos, China, Korea and Japan carried Pgd-13 and Ap-3 1 except var. inodorus in China. Among the latter two alleles, the frequency of Ap-31 was more than 50% in small seed type in north and east India, indicating that vars. makuwa and conomon related with small seed type in these areas. Their relationship was also indicated by the analysis of RAPD and CAPS in ethylene-related genes. Based on these results, the origin and differentiation of vars. makuwa and conomon was also discussed.