The waxy gene sequences including microsatellite sequence (CT)n and the part of first intron were amplificated and sequenced using the PCR pecific primers Wx-F / AG-2 for 252 rice landraces from 16 areas 64 counties of Yunnan. The results showed that Four variable sites were detected in the waxy gene sequences incuding 260 bases. The (CT)n variation duplicate number 10, 11, 12, 14, 16, 17, 18, 19, 20, 21 was tested at site 56 of the first intron upstream; The variation G / T was present in the first intron 1 site and T only was present in the cultivars with (CT)n length greater than 16 breeds; There were three variations include ATA / GTA /A at 86-88 site; There were two (AATT) n variations (5 and 6) duplicate number at 128 site. According to these four polymorphic sites, the 252 Yunnan rice landraces were classified into 16 genotypes, which Wx4 (32.54%), Wx9 (13.89%), Wx12 (12.7%), Wx5 (12.3%), Wx1 (8.33%), Wx11 (7.94%) were the main type, other types of frequency were lower. There were differentiation in genotype types and genotype frequencies between Indica / japonica subspecies, water / upland rice and sticky / glutinous rice. The indica / japonica, water / upland rice and no-glutinous / glutinous rice subspecies or ecotypes had exclusive genotype, shared genotype frequency also had differences. This indicated that genetic differentiation were occurred between subspecies or ecotypes. Geographical distribution of genotypes showed that Lincang, Puer genotype species were the most abundant, and expansion outward as it the center, genotype species were decreasing trend, the T at the first intron 1 site were mainly distributed in Lincang, Pu'er, Banna, Dehong and other southern regions. This study revealed the waxy gene the variability and distribution of Yunnan rice landraces groups.