Cucumis is the highly diverse genus of the family Cucurbitaceae. Two commercially cultivated species are Cucumis melo and Cucumis sativus. Sativus types are less diverse in fruit traits compared to melons. A group of melons commonly known as cucumbers due to their similarity in fruit traits with cucumbers of Cucumis sativus were cultivated in Karnataka, revealing high genetic diversity. To study the genetic diversity and structure within and between the species, 150 cucumis germplasm, including Cucumis melo and Cucumis sativus, collected from the different regions of Karnataka, were fingerprinted with 47 highly polymorphic Simple Sequence Repeat (SSR) markers, which were evenly distributed in the genome. Genetic diversity parameters among the collections revealed wide diversity among the melons compared to sativus types. A total of 602 alleles were identified through gel electrophoresis with a mean PIC value of 0.8. Based on the SSR data, a population structure analysis revealed the presence of four distinct populations, largely corresponding to species differentiation. The results showed that all sativus types, along with some melons, were grouped in Population 2, while the remaining melons were grouped into three distinct populations, indicating a high degree of heterogeneity in the base population of melons, while the lowest degree was seen in sativus types. The AMOVA result showed that the percent of genetic variation among and within Cucumis species is 78 percent, and between populations, it is 12 percent. The highest Fis value of 0.881 indicates the maximum extent of genetic similarity among the collections, and the Fst value (0.118) revealed less diversity among the populations. The highest Nei’s genetic identity was between Population 4 and Population 3 (0.639), indicating gene flow during evolution, and the maximum genetic distance was between Population 1 and Population 2 (0.734) among the four populations, indicating that individuals of both the populations are highly diverse. Admixtures between the populations are evidence of hybridization and migration during the evolution of species. The present findings of the genetic structure of Cucumis species revealed the existence of a wide diversity in melons that could aid in the exploitation for the development of improved varieties and species conservation.