Biogeographical regionalization schemes have traditionally been constructed based on taxonomic endemism of families, genera, and/or species, and rarely incorporated the phylogenetic relationships between taxa. However, phylogenetic relationships are important for understanding historical connections within and among biogeographical regions. Phylogeny-based delineation of biota is a burgeoning and fruitful field that is expected to provide novel insights into the conservation of regional diversity and the evolutionary history of biota. Using the Chinese flora as an example, we compared regionalization schemes that were based on: (1) taxonomic endemism, (2) taxonomic dissimilarity, and (3) phylogenetic dissimilarity. Our results revealed general consistency among different regionalization schemes and demonstrated that the phylogenetic dissimilarity approach is preferable for biogeographical regionalization studies. Using the phylogenetic dissimilarity approach, we identified five phytogeographical regions within China: the Paleotropic, Holarctic, East Asiatic, Tethyan, and Qinghai–Tibet Plateau Regions. The relationship of these regions was inferred to be: (Paleotropic, ((East Asiatic + Holarctic) + (Tethyan + Qinghai–Tibet Plateau)).