Genetic diversity of 257 representative melon germplasms from various regions in China was studied based on the investigation of 20 morphological characters. The results showed that the obvious difference was observed with the seven qualitative characters (fruit shape, ground color of fruit skin, vein color of fruit skin, vein shape of fruit skin, flesh color, flesh texture, and seed coat color) and the six quantitative characters (fruit diameter, fruit length, fresh weight of single fruit, thickness of fruit flesh, soluble solid content, and 1000-seed weigh). The Shannon’s indices of the seven qualitative characters and the six quantitative characters exceeded 1.00 and 1.50, respectively. The mean Shannon’s index of all the melon germplasms reached to 1.09, and the degree of genetic diversity between various regions was distinctly different. The upper-to-lower older of Shannon’s index for the various regions was: Northwest China, Central China, East China, North China, Northeast China, and South China. Principal coordinate analysis (PCO) divided all the melon germplasms into three regions, i.e. dominant region for thick germplasms, mixed-distribution region for chick/thin germplasms, and dominant region for thin germplasms. The melon germplasms from various regions distributed differently in the PCO diagram; the thick germplasms from Northwest China widely distributed cross the three regions and revealed higher genetic diversity, so did the thin germplasms from Central China and East China. Our result supports the view that Sinkiang is considered as a second origin center of thick melon, and Huanghuai and Changjiang River zone is considered as a primary origin center of thin melon.