Incarvillea is a genus with considerable ornamental and medicinal value, yet many of its 16 species are threatened in the wild and two (Incarvillea forrestii and Incarvillea altissima) may be extinct. An extensive field survey of the Chinese species has shown that logging is the greatest threat to woodland margin species, while overgrazing by cattle endangers species from alpine meadows. To aid the setting of conservation priorities, we used phylogenetic weighting of species, based on the molecular phylogeny of both nuclear (nrITS) and chloroplast (trnL-F region) gene regions. We estimated molecular diversity with measures for genetic diversity (GD) and phylogenetic diversity (PD). PD/GD values highlighted the importance of Incarvillea sinensis and two Central Asian species, Incarvillea semiretschenskia and Incarvillea olgae from Kazakstan and Kirghizia, for which little is known. This combination of phylogenetic and complementarity analyses focused on the provinces of Sichuan, Yunnan, and Qinghai, with Yunnan having the only adequately protected areas for that genus.