Leptosiphon Benth. (Polemoniaceae) has 40 taxa, distributed mainly in western North America, with one species in Chile. Phylogenetic studies of Polemoniaceae have consistently supported recognition of Leptosiphon as a separate genus from Linanthus, and resolved an array of taxonomic problems; however, several issues remained unclear for Leptosiphon. In those studies, sampling of Leptosiphon was incomplete, and certain species having strikingly similar floral morphologies appeared non-monophyletic, while other species groups with divergent floral morphologies formed a clade. Our analyses use greater sampling across taxa in Leptosiphon and, in addition to nrITS, the non-coding chloroplast region trnS–trnG to help resolve the genus phylogeny. These results yielded a more complete phylogeny from which to base further research on floral evolution in this group. However, much work remains to be done in resolving species level relationships. Analyses of morphological character evolution suggest that several characters that have been used to define sections within Leptosiphon are misleading. In addition, these data suggest that at least one species (i.e., L. parviflorus) might be polyphyletic.