Four hundred and seventy-seven accessions of the second core collection of rice landrace from five rice cropping regions (16 prefectures) of Yunnan Province, China, were evaluated for cold tolerance at booting stage. The results showed as follows: 1) there was a significant positive correlation (0.588**) between anther length and seed setting rate under natural low temperature conditions but was not significant in greenhouse (0.080). 2) there were significant differences in cold tolerance among cora collections from different cropping regions under natural low temperature conditions while a negligible cold damage in greenhouse (with a seed setting rate approaching or exceeding 70%) for cold tolerance evaluation. Cold tolerance of core collection from Northwest Yunnan cold highland japonica region was the strongest, and that from south marginal paddy-upland rice region was the most sensitive, suggesting that the breeding goals for cold tolerance should be different in various rice cropping regions. 3) there were remarkable differences in cold tolerance of core collections from different prefectures of Yunnan Province under natural low temperature conditions. Based on the reduction of seed setting rate and characteristics of natural climate, the 16prefectures could be divided into three categories, i.e. serious cold damage, cold damage and slight cold damage regions. 4)Difference of cold tolerance between different rice cropping regions and prefectures revealed further that temperature change caused by elevation and latitude was not only a dominant factor for differentiation of japonica and indica but also the basic reason that the genetic diversity and six ecological group of indica and japonica were being developed and, even the critical factor leading to the formation of the cold tolerance gene as well. The cold tolerance at booting stage could be believed to be resulted from the long term co-evolution between Yunnan rice landrce and cold stress in rice cropping regions.