The phylogenetic relationship and genetic diversity among 145 melon accessions，including 117 China’s Xinjiang landraces and 28 exotic melon germplasms collected from abroad and eastern China, were analyzed based on sequence-related amplified polymorphism technique (SRAP). Two-hundred and twenty-four bands were identified by 20 pairs of SRAP primers in total. Among them, 216 bands were polymorphic with the polymorphic rate 96%. And 11.2 bands and 10.8 polymorphic bands were amplified by each pair of primer on average. The polymorphism information content (PIC) with each pairs of primer was between 0.73 and 0.94, and the average was 0.85. The genetic diversity index (H) and Shannon's information index (I) of accessions in different ecological regions ranged from 0.1075 to 0.2560 and from 0.1569 to 0.4061, respectively. Whether H and I of southern Xinjiang, eastern Xinjiang or northern Xinjiang, which were higher than other ecological regions, in which the southern Xinjiang was highest. These results suggested that there was rich genetic diversity among the melon landraces collected from various parts of Xinjiang. The values of genetic identity and genetic distance between any two distinct ecological regions were 0.6384-0.9919 and 0.0081-0.4488, respectively. The values of genetic identity were above 0.95 among northern Xinjiang, southern Xinjiang and eastern Xinjiang, and in which the values of genetic distance were below 0.04, the genetic differentiation in three ecological regions was low. The relationship of melon accessions which are from Xinjiang of China, Western Asia, India and Spain were near with each other while it had a distant relationship for Xinjiang with Korea, Japan, the Untied States and the former Soviet republics. Three groups were clustered for 145 melon accessions according to genetic similarity coefficient of 0.548. There is no distinct boundary between thick-skinned melon and thin-skinned melon. The genetic relationship of thick-skinned melon and thin-skinned melon is quite different with different germplasm materials. 117 China’s Xinjiang landraces can be divided into four categories and six subgroups, as A（Ⅰ～1），B（Ⅰ～2，Ⅰ～3，Ⅰ～5），C（Ⅰ～6）and D（Ⅱ），which is different from the clustering result based on SRAP markers and the classification result according to the characters of melon mature period, the fruit shape and fruit surface. But the melon accessions which belong to the same variety or cultivar group are tending to in the same cluster in the clustering result based on SRAP markers.