For the last 150 years, the taxonomy of Hoffmannseggia has been variously entangled with Caesalpinia and Pomaria. Traditionally, Hoffmannseggia consisted of herbaceous or sub-shrubby perennials (rather than trees or vines) that lack spines and usually bear glandular trichomes on portions of the vegetative surfaces. However, the lack of correspondence of other characters such as flower shape, fruit type, and sepal persistence with habit and armament led to the repeated realignment of various species. Recent molecular work has shown that Hoffmannseggia forms a monophyletic group supported with several morphological synapomorphies and that it is not closely related to either Caesalpinia or Pomaria. Here we use molecular data from the nuclear ITS spacer regions, the trnL spacer and trnF intron chloroplast regions, and the rbcL gene to examine the relationships of Hoffmannseggia species. We show that there are two major clades in the genus that do not correspond to any previous infrageneric taxonomy. These clades are supported by morphological differences, the most striking of which is habit with one clade consisting of sub-shrubby species and the other of herbaceous species. We point out other characters that support subgroups within these clades, document one case of hybridization, and identify other suspected cases of hybridization. We also make the new combination Hoffmannseggia pumilio.