The genus Polemonium is composed of animal-pollinated herbs found largely in North America. Wide phenotypic variation suggests rapid evolution of floral and vegetative morphology. However, phylogenetic relationships within Polemonium have received little attention. We present a phylogeny of Polemonium based on 1676 Amplified Fragment Length Polymorphisms (AFLPs). We obtained similar topologies through minimum evolution analysis using Nei-Li genetic distances and parsimony analysis. Our analyses supported the mono-phyly of most species, and indicated that the single annual species, P. micranthum, is sister to all perennial species. Relationships were well resolved among species separated by genetic distances<0.16. Three well-supported clades each included taxa from one of three species complexes: the P. caeruleum complex, the P. pulcherrimum complex, or the P. viscosum complex. Relationships within clades were generally consistent with earlier systematic work. Exceptions were the inclusion of eastern North American P. reptans within the P. caeruleum clade, inclusion of P. boreale within the P. pulchernmum clade, and a close relationship between tetraploid P. califomicum and diploid P. pulchernmum subsp. delicatum. Our results indicate that floral traits are quite divergent among close relatives within the genus, and provide a phylogenetic framework for research on adaptation and speciation in Polemonium.