A total of 416 varieties being grown during 2007-2008 in 56 counties in Yunnan province were evaluated using 20 pairs of SSR markers. Total of 116 alleles were detected and the number of alleles per marker ranged from 3 to13, with an average of 5.8. The mean of polymorphism information content (PIC) of SSR markers was 0.681, with a range from 0.349 at RM18 to 0.891 at RM6748. PIC varied from 0.025 to 0.679 among the 56 counties, with an average of 0.381, that of Menghai was the highest while that of eight counties in each only one accession being collected was the lowest. Cluster analysis with UPGMA method based on genetic identity (GI) indicated that 56 counties were classified into 3 groups at GI of 0.362, GI was 0.943, the highest between Mouding and Yao’an counties while that was the lowest between Simao and Ninglang counties, with GI of 0.033. GI was related to geographical regions among 56 counties. Rich genetic diversity exists in Yunnan rice landraces in present production. Genetic diversity of landrace rice distribute uniformly between prefectures in Yunnan province and rich genetic diversity mainly concentrate in five prefectures including Xishuangbanna, Dehong, Puer, Lincang and Honghe.