Phylogenetic relationships among the 16 series within Iris section Limniris were reconstructed based on chloroplast sequence data using maximum likelihood and Bayesian inference methods. Section Limniris is polyphyletic as currently delineated because series Spuriae, Foetidissimae, Syriacae, Longipetalae, Vernae, Unguiculares, and some elements of Tenuifoliae are placed outside of the core group of Limniris species. The most inclusive monophyletic clade of Limniris species includes the series Californicae, Sibiricae, Laevigatae, Tripetalae, Prismaticae, Ensatae, Ruthenicae, Hexagonae, and Chinenses, and I. songarica. Within the core Limniris clade series Sibiricae, Tripetalae, and Chinenses are polyphyletic whereas Laevigatae is paraphyletic. With one exception, species within the core Limniris group are distributed in either Asia or North America, with a few Asian species extending into Europe and for the most widespread species, Iris pseudacorus (series Laevigatae), into northern Africa with naturalized populations in North America. The one exception is I. setosa with a native range that includes both eastern Asia and North America.