Desmanthus is currently included in the Dichrostachys group of the tribe Mimoseae along with three other genera having sterile basal flowers: Dichrostachys, Neptunia, and Gagnebina. Historically, Desmanthus has often been distinguished by lacking characters present in the other genera: the short shoots or stipular spines with persistent fused stipule bases of Dichrostachys, the linear, basifixed anthers of Gagnebina, and the seismonastic leaves and unique floral development of Neptunia. A comparison of Desmanthus with the sister genera indicates that subulate stipules and peltate floral bracts may be synapomorphies of Desmanthus. A cladistic analysis of Desmanthus and Calliandropsis, using Dichrostachys, Gagnebina, and Neptunia as outgroups, supports the segregation of Calliandropsis from Desmanthus. The cladistic analysis also suggests that Neptunia may be a derived element from within Desmanthus and that Dichrostachys may be paraphyletic to Desmanthus. A study of seedling morphology in Desmanthus showed four different seedling types. These types can be used to identify species but are too plastic to be useful in higher-level classification. Scanning electron microscopy was used to observe microcharacters of the pollen and seeds. Pollen features are too invariant within Desmanthus to help resolve species relationships but are informative about generic relationships. Characters of the seed coat are important in distinguishing one infrageneric group and pleurograms in distinguishing several species. Nyctinastic leaf movements also provide valuable species and phylogenetic characters. A morphometric analysis of the Desmanthus virgatus complex was done using 19 population samples, 15 of them grown in a common garden. Based on this and other data, five species rather than four varieties are recognized in the D. virgatus complex. Desmanthus comprises 24 species, including four varieties. One new variety is described, D. pumilus var. michoacanus. Two new combinations are proposed, D. glandulosus and D. tatuhyensis var. brevipes.