A total of 601 accessions of representative on-farm conservation rice landraces from 15 prefectures of Yunnan in two different periods (1980 and 2007, respectively) were cellected to dissect the phenotypic variation and the Shannon-Wiener diversity index (H′) difference. Totally, thirteen agronomic traits were phenotyped in Xishuangbanna Yunnan and Sanya Hainan, i.e. days to heading, plant height, panicle length, panicle number per plant, spikelet number per panicle, seed setting rate, 1000-grain weight, grain length, grain width, ratio of length to width for grain, panicle exsertion, flag leaf length and flag leaf width. Days to heading, plant height, spikelet number per panicle, grain width, ratio of length to width for grain and panicle exsertion showed significant or even highly significant difference between the two periods. In addition, days to heading, spikelet number per panicle, and ratio of length to width for grain of population collected from 2007 (named G2 population) were higher than that from 1980 (named G1 population). By contrast, the means of plant height, grain width, and panicle exsertion from G2 population were higher. In these two planting places,, the coefficient of variations (CV) of the two populations showed non-significant difference, while the diversity index H′ showed significant difference in Yunnan. In both planting places, the average H′ of different prefectures or cities showed non-significant difference between G1 and G2. In the two subpopulations collected from these two periods, the H′ (1.845/1.867) in 2007 was higher than in 1980 (1.791/1.830) in indica subpopulation, while it was higher in 1980 (1.898/1.888) than in 2007 (1.875/1.835) in japonica subpopulation. Japonica subpopulation was of higher H′ than indica subpopulation in both periods and planting places. All these results indicated that the phenotypic variation of on-farm conservation rice landrace varieties in 2007 was similar to in 1980. However, days to heading, spikelet number per panicle, and ratio of length to width for grain went up, while plant height, panicle exsertion went down. in addition,, the phenotypic diversity tended to be increasing.