SSR markers derived from expressed sequence tags (EST-SSR) are valuable tools for genetic variation assessment because they potentially exhibit functional diversity. The genetic variations of 27 melon accessions, including 21 thin-skinned melon landraces which nearly represent all types of thin-skinned melon landraces originated in China, were analyzed with EST-SSR markers. Of the 22 EST-SSR markers employed, 19 EST-SSR detected polymorphism with 13 of which had putative functions. The number of alleles detected by EST-SSR ranged from 2 to 5 with the average of 3. The PIC value for each locus varied from 0.21 to 0.68 with the mean of 0.46. Cluster analysis by UPGMA partitioned the accessions into groups of thin-skinned melon and thick-skinned melon with high bootstrap value. In the thin-skinned group, the EST-SSR markers failed to discriminate the thin-skinned vegetable melon from the other thin-skinned melon accessions.