Premise: Biodiversity is often only measured with species richness; however, this metric ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan.

Methods: We compiled a community data set of 1239 grid cells (20 × 20 km each) including 672 taxa based on >300,000 specimen records. We combined the community data with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid cells with conservation zones and range maps of native Japanese deer.

Results: Taxonomic richness was highest at mid‐latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid‐latitudes. Grid cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics.

Conclusions: Our integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple metrics when establishing conservation priorities.