Many species of the subfamily Polygonoideae are economically important. However, phylogenetic relationships and taxonomic treatments of these species remain disputed. In this study, we used highly orthologous nuclear genes and plastome sequence variation extracted from transcriptomes from 98 species of 26 genera of Polygonaceae mainly from the subfamily Polygonoideae to construct a robust phylogeny. We discerned six successively diverged and well-defined clades and both nuclear and plastome phylogenies are highly consistent with each other in this subfamily. Phylogenetic relationships between all clades and subclades were well resolved within Polygonoideae. Our analyses revealed that the shrub tribe Atraphaxideae and the herbal genera Polygonum, Persicaria, and Fallopia are polyphyletic. The sampled species of Polygonoideae started to diversify around the Cretaceous/Tertiary boundary (70?Ma) when the global climate exhibited large oscillations. Further origins of more herbal and woody species were found to have clearly increased during later climatic oscillations. We found that woody habits, especially shrubs, originated multiple times from ancestral herbs in this subfamily. Local dry climates may have favored such habit shifts from ancestral herbs. Our results deepen our understanding of evolutionary diversification of Polygonoideae.