Pugionium (Brassicaceae) is a small genus occurring in the Central-Asian deserts. The interspecific delimitation and taxonomic treatments of this genus are disputed and its phylogenetic origin remains elusive. In this study, we examined these issues based on the morphological and molecular data obtained for the first time. We used statistical methods to examine interspecific and intraspecific morphological variations and the results suggested that only two species, P. dolabratum and P. cornutum, can be warranted for all examined populations and specimens while the three species (P. calcaratum, P. cristatum and P. pterocarpum) should be incorporated into P. dolabratum. This delimitation was further supported by the molecular data: all populations of P. dolabratum, P. calcaratum, P. cristatum and P. pterocarpum shared the same ITS genotype while those from P. cornutum had the other type. Phylogenetic analyses of Pugionium and representative genera of Brassicaceae based on ndhF sequences suggested that this genus was sister to the genus Megacarpaea, which together comprised a well supported lineage with Farsetia, Lobularia, Iberis and Ionopsidium, while other two genera (Isatis and Bunias), which were previously suggested to be closely related to this genus, were placed in the other lineages. We further discussed the origin of this genus and suggested that it probably originated in the central Asia when the climate became arider since the late Miocene.