A total of 1189 newly collected rice landraces from 16 prefectures (cities) of Yunnan were used to study difference and distribution of the diversity index for rice landraces by 17 agronomic traits. The results showed that the diversity indexes in counties Mangshi, Yingjiang, Longchuan, Tengchong, Menghai and Cangyuan ranged from 1.6010 to 1.6822, which were higher than that of other counties. The diversity indexes in prefectures Dehong (1.6951), puer (1.6746) and Lincang (1.6723) located in south and southwest parts of Yunnan were higher than that of other prefectures. At rice ecological zone level, the diversity indexes of yield related traits (number of effective panicles, number of spikelets per panicle, thousand-grain weight and seed setting rate) and biological traits (plant height and grain length) were slightly higher in southern lowland and upland rice zone (II) than in northwest highly cold japonica rice zone (III) and southern single and double cropping indica rice zone (I). No significant difference on diversity indexes of 17 traits were observed among zones I, II, and III, while the diversity indexes of 5 traits (seed setting rate, grain width, grain length/width ratio, flag leaf length and flag leaf width) were significantly different between zone II and northeast plateau japonica rice zone (V). The diversity indexes of 13 traits (except for flag leaf angle, lodging, grain color and leaf hair) were significantly different between zone II and central single cropping indica or japonica rice zone (IV). At nationality area level, the diversity indexes of nationalities Hani, Han, Jingpo and Yi ranged from 1.7033 to 1.7308, which were higher than that of other nationalities. In the same prefecture, the average diversity indexes in Dehong prefecture with nationalities Jingpo (1.3735), Lisu (1.3714) and Han (1.3526) were high. In the same nationality zone, the average diversity indexes in prefectures Dehong, Baoshan, Lincang and honghe were high (1.6190-1.6808). 173 accessions with big panicles and 84 accessions with big grains were found mostly in prefectures Dehong, Xishuangbanna and Puer. The accessions with slender grains were mainly distributed in prefectures Dehong and Lincang. Taken together, the prefectures and counties in south and southwest of Yunnan province were found to be a diversity center of rice landraces.