Astragalus is a species-rich genus occurring in the western arid habitats in China and its diversification and infrageneric relationships in this region remain unclear. In the present study, based on molecular data, we aim to (i) test whether Phyllolobium (previously treated as a subgenus Pogonophace in Astragalus) should be warranted; and (ii) date the origin of Phyllolobium and probable diversification of Astragalus sensu stricto (s.s.). We sequenced five species from Phyllolobium first and collected all related sequences from the genus, Astragalus s.s and their close relatives (Oxytropis and Caragana etc.). Our phylogenetic analyses suggested that all species of Phyllolobium comprise a monophyletic sister-group to genera of the subtribe Coluteinae. Molecular dating suggested that Phyllolobium and Astragalus s.s. originated around 8 and 10 million years ago. These two estimates are highly consistent with the intense uplifts of the Qinghai-Tibetan Plateau inferred from geological evidence. In addition, one section of Pogonophace (Sect. Robusti) was estimated to originate 2.5 million years ago and this section with a tendency for dry habitats seems to be evidence of Asian intensified aridity resulting from the intense uplift of the Qinghai-Tibetan Plateau.