Genetic diversity of commercial and local rice cultivars in Yunnan Province was studied using the resistance gene analogue (RGA) based on resistance gene conserved sequences. The RGA analysis of 137cultivars was conducted by PCR amplification using three primers, i.e. S1/AS3, XLRR for/XLRR rev, and Pto-kin1/Pto-kin2, respectively. The results showed that both Indica and Japonica cultivars were genetically highly diverse. All cultivars were divided into 3 lineages according to the DNA band data at 96% dissimilarity,and into 20 lineages at 60% dissimilarity. The lineages were related to their genetic background and blast disease resistance with only a few exceptions. The RGA data can be useful in rice production by mixed-planting of different cultivars in the field and breeding of resistance cultivars by selecting different parental cultivars with great genetic diversity.