Oxalis subg. Thamnoxys is a mostly South American group of Oxalis encompassing almost 80 species from tropical habitats that are currently separated into nine sections based on morphology and geographic distributions. In this study, we investigated whether Oxalis subg. Thamnoxys and its sections are monophyletic. DNA sequences of the nrITS, trnL-trnL-trnF , and petA-psbJ from 92 specimens of Oxalis (55 from O. subg. Thamnoxys , 37 from O. subg. Oxalis , and five outgroup taxa) were used to investigate phylogenetic relationships among its nine sections. Nuclear and plastid molecular markers were subjected to maximum likelihood and Bayesian inference analyses individually and in a combined data matrix. Our phylogenetic trees recovered O. subg. Thamnoxys as monophyletic only if O. praetexta , previously included in O. sect. Robustae , is transferred to O. subg. Oxalis. The remaining samples of the subgenus emerged in a clade with full bootstrap and posterior probability support. Within it, O. sect. Holophyllum was the only section that was recovered as monophyletic, whereas the remaining sections were not, either because of sampling a single species of each (O. sect. Foliosae , Hedysaroideae , and Phyllodoxys), to the unexpected placement of O. goyazensis (O. sect. Robustae) in O. sect. Psoraleoideae , or to the sister relationship between O. densifolia (O. sect. Foliosae) with O. pyrenea var. macrochaeta (O. sect. Thamnoxys), suggesting the need of revaluating some specific affinities and updating sectional circumscriptions. This phylogenetic study with an improved sampling of O. subg. Thamnoxys is the first step towards an updated classification of the subgenus and for interpreting both its morphological diversification and biogeographic history in South America. [ABSTRACT FROM AUTHOR]