Environmental variables, such as ambient energy, water availability, and environmental heterogeneity have been frequently proposed to account for species diversity gradients. How taxon-specific functional traits define large-scale richness gradients is a fundamental issue in understanding spatial patterns of species diversity, but has not been well documented. Using a large dataset on the regional flora from China, we examine the contrast spatial patterns and environmental determinants between pteridophytes and seed plants which differ in dispersal capacity and environmental requirements. Pteridophyte richness shows more pronounced spatial variation and stronger environmental associations than seed plant richness. Water availability generally accounts for more spatial variance in species richness of pteridophytes and seed plants than energy and heterogeneity do, especially for pteridophytes which have high dependence on moist and shady environments. Thus, pteridophyte richness is disproportionally affected by water-related variables; this in turn results in a higher proportion of pteridophytes in regional vascular plant floras (pteridophyte proportion) in wet regions. Most of the variance in seed plant richness, pteridophyte richness, and pteridophyte proportion explained by energy is included in variation that water and heterogeneity account for, indicating the redundancy of energy in the study extent. However, heterogeneity is more important for determining seed plant distributions. Pteridophyte and seed plant richness is strongly correlated, even after the environmental effects have been removed, implying functional linkages between them. Our study highlights the importance of incorporating biological traits of different taxonomic groups into the studies of macroecology and global change biology.