Internal transcribed spacer (ITS) nrDNA sequences of 42 accessions (representing 28 species) of Aframomum revealed an unusually low level of sequence variation, suggesting a recent radiation of the genus in Africa. The sample of species analysed includes all the main morphological variation and is based on wide geographical sampling. The Aframomum sequences varied from 187bp to 190bp (ITS 1) and 215bp to 216bp (ITS 2). Pair-wise sequence difference between accessions varied from 0% (e.g. A. luteoalbum and A. thonneri) to 2.74% (e.g. A. sp. nov. B to A. pseudostipulare). This contrasts with a comparable data set for the SE Asian genus Alpinia in the same tribe (Alpineae) in which maximum pair-wise difference is six times greater (range 0.5–15.6%). A parsimony analysis of the in-group and out-group taxa supports the monophyly of the genus Aframomum, but does not resolve the relationships between the in-group species. Four putative multi-species groups, however, have some jackknife support. The species sampled vary greatly in vegetative, floral and fruit characters. This morphological variation is not reflected in the ITS sequence data. This may be a result of rapid radiation under conditions of Pleistocene climatic change and effective dispersal of seeds by primates.