Based on the pollen and spores data of thirty-five soil surface samples and twenty-eight profile samples from seven sampling plots of community forests in the sourthern subtropics of Yunnan province, the characteristic of pollen and spores spatial assemblages and its relationship with different environments are analyzed. Results show that: (1) There are significant differences in the pollen and spores taxa, amounts, dominant taxa and plant florae between both flanks of the Ailao Mountain. The pollen and spores taxa and amounts of the western part are more plentiful than the eastern. The dominant taxa are more centralized and prominent in the eastern part of the Ailao Mountain, while they are not prominent but more complex in the western. As for plant florae distribution, there are great differences in the amount and proportion of the four florae of cosmopolitan, pantropic, tropical Asia, tropical Africa and north temperate between the eastern and the western flanks. (2) The analysis of profile pollen and spores assemblages shows that their changing trends are basically in the accordance with the surface pollen and spores assemblages, also an indication of the differences between the both flanks. (3) Such obvious spatial differences of the pollen and spores assemblages are relevant to the regional terrains and climatic differential characteristics. The barrier function of the vertical mountain range and the different monsoon circulations which respectively come from Pacific Ocean and Indian Ocean that result in different hydro-thermal characteristics are mainly attributed to regional differentiated patterns of the pollen and spores assemblages, indicating the regional differentiation of the natural environment in the southern subtropics of Yunnan province.