A total of 64 simple sequence repeat (SSR) markers were used to investigate the genetic diversity of 96 rice landraces and improved varieties from Yunnan; all of the 64 SSR loci were polymorphic. A total of 741 alleles were detected. Each locus contained 2-29 alleles, for a mean of 11.57 alleles; the mean genetic diversity index (He) of Nei was 0.56, with scope from 0.345 (RM321) to 0.932 (RM1). The genetic diversity of the rice varieties from Yunnan was not evenly distributed according to geographical locations. Two distinct groups (indica and japonica rice) were identified for the 96 rice varieties, with a similarity coefficient of 0.17. There was no significant difference in SSR diversity between indica and japonica subspecies. The mean number of alleles (Ap) and mean Nei genetic diversity index for indica rice (Ap=10.6, He=0.46) were close to those of japonica rice (Ap=10.7, He=0.48). The similarity of these indices may be related to a certain frequency of the gene exchange. Non-glutinous rice and glutinous rice were scattered in the rice group, and the genetic basis of cultivated rice may be from these local varieties. Yunnan cultivated rice can be distinguished by SSR markers, and the genetic diversity of rice landraces from Yunnan is rich. A large number of highquality
characters are available for selection in rice breeding.