Sugarcane parents are important genetic resources for genetic breeding and innovation of sugarcane. In order to learn the genetic diversity of Yunnan commonly-used parents, about sixty three clones were screened by using 30 pairs of high polymorphic SSR primer with ten origin species as outgroup. The results showed that total 363 bands were obtained by these SSR primers, of which 353 were polymorphic bands. High Percentage of polymorphic bands and Polymorphism information content (96.97% and 0.9441) indicated Yunnan commonly-used parents possess rich genetic diversity. The analysis of Jaccard similar coefficient of all clones illustrated the big genetic differences appeared among these parents with a low average similar coefficient of 0.4309(range between 0.2804-0.7329). These parents from main land of China exhibited the biggest genetic differences, followed by these parents from foreign countries. By using UPGMA cluster method, all parents can be assigned into two groups of different sizes. Moreover, the big group containing most of parents also can be segregated into two subgroups. Based on the results of clustering, some parents from main land of China, which are not only excellent parent but also main cultivar, performed a close genetic relationship. And this relationship is also found between these parents from foreign countries and some old parents from main land of China. Finally, these results mentioned above will improve the exploring efficient of Yunnan commonly-used parents and provide an important direction for screening parent and making cross combination in breeding and innovation programs.