Three series, Prismaticae, Tripetalae, and Laevigatae, in Iris subgenus Limniris comprise a clade of nine species with an affinity for wetland environments. Prior work has failed to resolve phylogenetic relationships among these taxa. We used maximum likelihood and Bayesian inference methods to analyze plastid and nuclear ribosomal ITS sequence data to infer a robust phylogeny for this circumboreal group. Our analyses recovered clades that do not reflect current series circumscriptions and show that species from Tripetalae and Laevigatae comprise one clade. Species relationships also do not reflect geographic proximity, as Asian and North American species do not assort into regional clades. This finding suggests that multiple exchanges between Asia and North America are required to explain current distributions and refutes the hypothesis that Asian taxa are the earliest diverging lineage within the clade.