The parentage composition and molecular genetic diversity of 27 elite cultivars from Yunnan breeding unit were analyzed through pedigree and SSR molecular marker. The pedigree analysis of cultivars showed the parentage composition of these cultivars was made up of 24 germ plasm and their cytoplasm were mainly from Bandjarmasim Hitam(S.officinarum). Besides, old cultivars were similar to each other because they came from repeated crossing of a few key parents. For the newly developed cultivars, the number of their germ plasm has been increased by utilizing new elite parents. The molecular genetic diversity research indicated all cultivars possessed rich genetic diversity in 27 SSR locus and the UPGMA cluster of parentage composition was mainly similar to the molecular UPGMA cluster. In addition, between YZ99-601 and YZ65-55 exist a big difference in the molecular UPGMA cluster from these cultivars of the same crossing combination, so further identification is needed. YF82-682 and YF84-FB5 were also different from other cultivars because radiation of Co60 induced high genetic variance. It suggested those crosses between sugarcane cultivar within the same groups from cluster analysis and parentage composition should be avoided. The cultivars including more or new germ plasm should be utilized and the cultivars quite dissimilar to other cultivars should also be given a higher priority in breeding programs.