Gossypium L. is an economically important genus as it harbors four species that provide the cotton of commerce. Although many aspects of the evolution and taxonomy of Gossypium are well understood, there has been little work devoted to assessing relationships among Gossypium and its allied genera. In addition, newly discovered species, of Gossypium sect. Grandicalyx from Australia, have prompted a need for more research into the phylogeny of these new species and their relationships to other Gossypium taxa. Multiple data sets were used to address questions regarding (1) phylogenetic relationships among Gossypium and its relatives, and (2) the phylogeny and evolution of Gossypium sect. Grandicalyx. A protocol for handling multiple and sometimes competing data sets was developed, and was applied in the first study. This same protocol was not applicable for the second study, where amounts of sequence divergence were too low. Phylogenetic analyses of Gossypium and its allies indicated that Gossypium is a monophyletic group and that it is closely related to a clade represented by the Hawaiian genus Kokia and the east African/Madagascan genus Gossypioides. Phylogenetic inferences also suggested that Cienfuegosia may represent the first group to diverge during tribal radiation, and that Thespesia is not monophyletic. Studies of the Australian Gossypium sect. Grandicalyx showed that sect. Grandicalyx is monophyletic, with divergences inferred to be relatively recent. Molecular data sets provide little resolution with respect to the relationship among species within the section. Species are suggested to have radiated in the late Pliocene or Pleistocene after a much earlier (Miocene) divergence from the other extant Australian cottons. The palaeoclimatic record, sequence divergence estimates and phylogenetic data are congruent in suggesting a phytogeographic scenario for the diversification of species in sect. Grandicalyx, through range fragmentation of a more widely distributed ancestor or ancestors. This evolutionary history was accompanied by the development of a prostrate to reclining herbaceous habit, adaptation to seasonal fires, and a suite of features associated with myrmecochory.