Abstract:The spatial patterns and differentiation of species diversity of seed plants in Yunnan, China, were investigated based on distribution datasets of plant species at large scale, geographical information system and statistic methods. The results indicated that the discreteness of datasets of plant diversity and flora differentiation increased from families to genera and species. Compared with genera and species, the spatial variation and diversity centers of families were not obvious, which may be due to different historical periods in geology reflected by families, genera and species. The diversities of genera and species in southern Yunnan were richer than those of other areas except northwest Yunnan. The diversity centers of species were mainly observed in northwest Yunnnan, southern Yunnan, regions of Ailao Mountain, Wuliang Mountain, and Kunming region, which may be related to the geographical patterns of habitat heterogeneity and energy. Compared with families, the spatial variation of genera differentiation was more easily observed and showed similar patterns with species diversity, indicating significant correlation between plant diversity and flora differentiation. Compared with families, the centers of genera differentiation were obvious. On the whole, the spatial patterns of species diversity of seed plants and its differentiation were jointly shaped by habitat heterogeneity, energy and geological history.