This study constitutes the first investigation of cyanogenesis variation within the Turnera sidoides autopolyploid complex. The qualitative and quantitative analysis carried out in 38 populations showed that the five subspecies of the complex are cyanogenic, although the levels of cyanide released varied both between and within subspecies. Between the subspecies, carnea, holosericea and integrifolia showed higher values of HCN released than subspecies pinnatifida and sidoides. Within subspecies, there is a tendency toward an increment of mean cyanide values with ploidy levels and different hypotheses are considered in order to explain this variation. The study of cyanogenesis in populations from different geographical areas cultivated under uniform greenhouse conditions showed that, in the widespread subspecies pinnatifida, HCN variation may also reflect the action of different selection pressures, since populations having dissimilar cyanide levels grow in different phytogeographical provinces with different climatic regimes. On the other hand, the fact that the variation of HCN released was greater between populations from different geographical areas than that observed between diploid and tetraploid populations of the same area provides additional evidence for the multiple origins of polyploids of the T. sidoides complex. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 141, 85–94.