Molecular and morphological data have shown that Bombacoideae and Malvoideae together form a well-supported Malvatheca clade. Phylogenetic relationships in Bombacoideae have been studied, but some genera in Bombax s. l. have not been adequately sampled for sufficiently variable molecular markers. The relationships of Eriotheca, for example, have yet to be resolved. Here, nuclear (ITS) and chloroplast (trnL-F and matK) sequence data from 50 exemplars of Bombacoideae and seven additional taxa from other genera of Malvatheca were used to test monophyly of Eriotheca and its relationships with related genera of Bombax s. l. Parsimony and Bayesian analyses of individual and combined sequence data suggest that Eriotheca is not monophyletic as currently circumscribed but forms a paraphyletic grade containing Pachira s. l. The newly discovered Eriotheca Pachira clade has a probable synapomorphy of striate seeds. In addition, two other moderately supported clades emerged within the core Bombacoideae: Pseudobombax Ceiba s. l. and Bombax Spirotheca Pachira quinata. These three clades, and the African Rhodognaphalon together constitute the major clade of core Bombacoideae, whereas Adansonia appears to be more closely related to Catostemma, Scleronema, and Cavanillesia. The phylogenetic results imply three independent migrations from the New to Old World and homoplasy in staminal morphology.