The interpretation of the geographical patterns of cultivar diversity of rice is the essential basis for their protection. In this study, geographical patterns of cultivar diversity of rice and their correlation with environmental factors and culture of major nationality were investigated using GIS and statistical analysis. The results indicated that the centers of cultivar diversity were mainly observed in southern part of the studied area. Extremely significant correlation between proportions of population of Dai, Hani, Lagu and Bulang people and cultivar diversity of rice was found (P < 0.01), which may be due to their diet tradition, religion and production methods. Different cultural background played distinct roles in preservation of rice cultivar diversity. The cultivar diversity of rice was also strongly correlated with mean annual temperature and precipitation which were consistent with their floristic origin (P < 0.01). Significant correlation between altitudinal variation and cultivar diversity of rice in Southern Yunnan was found (P < 0.05). The geographical patterns of cultivar diversity of rice were strongly shaped by environmental factors and cultural background of major nationality. Cultural background played a direct role while environmental factors played indirect one.