Genetic diversity within populations of 16 rice landraces and 2 improved cultivars from Yunnan Province were analyzed using 20 SSR markers. The results showed that the SSR marker polymorphism within populations for 87.5% of rice landraces was higher than that of the improved cultivars, while the polymorphism within populations for 12.5% of landraces was similar with that of the improved cultivars. For 81.2% of rice landraces， the number of alleles (Na) and Nei’s genetic diversity index (He), were higher than those of the improved cultivars, and for 18.8% of landraces, the figures were same as or slightly smaller than those of the improved cultivars. The He within populations of rice landraces significantly differed, ranging from 0.0146 to 0.5117, while Huangbansuo1(Huangbansuo collected in 1980), Huangbansuo2(Huangbansuo collected in 2007), Maxiangu1(Maxiangu collected in 1980) and Maxiangu2(Maxiangu collected in 2007) were the highest with figures of 0.2327, 0.4214, 0.5117 and 0.4489, respectively. Heterozygosity within rice varieties for 87.5% of rice landraces was significantly higher than that of the improved cultivars. AMOVA showed that 1/4 genetic difference among rice landraces were from within populations of rice landraces (P<0.001). The polymorphism, Ne, He and percentage of variation within populations of rice landraces at RM333, RM257 and RM180 were higher than others. It was speculated that RM333, RM257 and RM180 were suitable for testing genetic diversity within rice landraces of Yunnan Province.
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