Axonopus P. Beauv. comprises nearly 90, mostly New World, species characterized by having spikelets with the inverse position (i.e., the backs of the upper glume and the upper lemma turned away from the rachis). The genus has been divided into four sections, five series, and three subseries, based exclusively on morphological features. Previous phylogenetic analyses based on a limited sampling of species showed Axonopus to be a monophyletic genus. In this study we increased the number of species sampled (46 species in the combined tree) and sequenced four DNA regions (external transcribed spacer [ETS], internal transcribed spacer [ITS], trnL-F, and ndhF). We tested the monophyly of Axonopus and its traditional infrageneric categories using parsimony, likelihood, and Bayesian inference. Additionally, we performed ancestral character state reconstructions of 45 morphological characters to infer autapomorphies of the species and synapomorphies for the genus and clades. Our findings confirmed Axonopus as a monophyletic genus only when Centrochloa Swallen and Ophiochloa Filg., Davidse & Zuloaga are included within it. Our analyses also showed that, with the exception of section Lappagopsis, infrageneric categories from previous classifications of the genus are artificial. Twenty-one morphological character states were identified as potential autapomorphies; two were reconstructed as potential synapomorphies for Axonopus, whereas 12 were reconstructed as potential synapomorphies for specific clades within the genus. Further molecular analyses, including sequencing of unlinked nuclear genes, are needed in order to reach a robust phylogenetic classification of the genus.