Abstract: Different latitudinal patterns of species diversity were given in previous studies and therefore mechanisms have been put forward to explain these patterns. However, there were significant discrepancies among related case studies. To test the effects of sampling scale on interpreting these discrepancies, we explored latitudinal patterns of species diversity at regional and community scales in northwestern Yunnan. Based on literature data as well as our field investigations, community and regional datasets were established, including the species richness of 68 plots at the community scale and that of seed plants in 26 counties at the regional scale, respectively. Based on these two datasets, the relationship between species richness and altitudinal gradient, as well as climatic and geographical factors, was analyzed using bivariate correlations analysis and stepwise regression. Our results showed that plant species diversity decreased with increasing latitude at the community scale, which was mainly correlated with the thermal factor. Contrarily, an increasing trend was observed with the increase of latitude at the regional scale, which was mainly due to altitude difference per unit of area. The results demonstrate the influence of sampling scales on the estimation of plant species diversity distribution. In conclusion, when determining the hotspots of plant diversity in northwestern Yunnan, we should analyze the data collected at different sampling scales to eliminate blind spots in biodiversity protection.