BackgroundPyrostria sensu lato (s.l.) is regarded as one of the polyphyletic group within Vanguerieae formerly comprising of Pyrostria sensu stricto (s.s.), Pyrostria group A and Pyrostria group B delineated by the number of locules and geographical occurrence. Recent molecular phylogenetic studies within the genus have narrowed its circumscription that resulted in the merging of Pyrostria group A and Pyrostria s.s. Although some species of Pyrostria group B were already transferred to Pyrostria s.s. and Psydrax based on morphology, other representatives of the group remain unsettled.ResultsBayesian and parsimony analysis of the combined ITS (nrDNA) and trnL-F (cpDNA) datasets showed a well-supported clade of the whole Vanguerieae containing four Philippine endemic representatives of Pyrostria group B. The placement of Canthium oligophlebium, Canthium obovatifolium and Canthium ramosii within Pyrostria s.s. (PP = 0.99; BS = 85%) is robustly supported likewise the affiliation of C. gynochthodes with Psydrax (PP = 0.94; BS = 85%). Morphological features shared by our species with Pyrostria s.s. and Psydrax further supports our molecular data.ConclusionOur study supports the earlier hypothesis that Canthium oligophlebium, C. obovatifolium and C. ramosii should be placed under Pyrostria s.s. except for C. gynochthodes that grouped with Psydrax. Four new combinations are proposed in this study. The generic affiliations of other species of Pyrostria group B should be reinvestigated towards a more natural classfication in Vanguerieae.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-014-0065-3) contains supplementary material, which is available to authorized users.