Relationships among the roughly 55 species of Iris subgenus Scorpiris have been studied. A matrix of six plastid DNA regions (matK, rpl14-rps8 spacer, infA-rpl36 spacer, trnE-trnT spacer, trnL intron and trnL-F spacer) was produced from 57 accessions (52 taxa) and analysed with both parsimony and Bayesian methods. Five major clades are identified, of which four have strong geographical correlations, whereas the fifth corresponds to Iris section Physocaulon. In our results, several species are placed with species not previously considered to be related, although, in some cases, there are morphological characters that suggest that these newly indicated relationships are reasonable. For some of the other oddly grouped species, we can only assume that remarkable parallelisms in morphology have occurred or hybridization is involved. Presently, with plastid DNA as our only comprehensive data resource, we are not able to evaluate more thoroughly these more puzzling associations of species. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 281–300.