The Bouteloua curtipendula complex (Poaceae: Chloridoideae) has been treated as a group of 12 species distributed from Canada to Argentina. Due to considerable morphological variation, putative hybridization, polyploidy (including aneuploidy), and apomixis, circumscription of and relationships among taxa have been uncertain. To infer the phylogeny of this complex, two non-coding regions, the internal transcribed spacer (nrDNA) and trnT-L-F (cpDNA), were sequenced and analyzed by maximum parsimony and maximum likelihood methods. Character-state reconstruction was carried out to test the utility of morphological characters used for species circumscription. Nuclear and plastid data revealed similar phylogenetic patterns, albeit with a lower level of resolution from the trnT-L-F sequences. Results support monophyly of the Bouteloua curtipendula complex, but not the species monophyly, except for B. triaena, which forms a strongly supported clade in both phylogenies. The origin of the Bouteloua curtipendula complex seems to be recent with low divergence between taxa. All of the morphological characters used to circumscribe species were found to be homoplasious.