Phylogenetic analyses are used to examine the morphological diversity and systematics of Synthyris and Besseya. The placement of Synthyris and Besseya in Veronicaceae is strongly supported in parsimony analyses of nuclear ribosomal ITS DNA sequences. Parsimony and maximum likelihood (ML) criteria provide consistent hypotheses of clades of Synthyris and Besseya based on the ITS data. The combination of morphological characters and ITS data resolve additional clades of Synthyris and Besseya. The results show that Synthyris is paraphyletic to Besseya. In the monophyletic Synthyris clade, Besseya forms part of a Northwest clade that also includes the alpine S. canbyi, S. dissecta, and S. lanuginosa and mesic forest S. cordata, S. reniformis, S. platycarpa, and S. schizantha. The Northwest clade is the sister of S. borealis. An Intermountain clade, comprising S. ranunculina, S. laciniata, S. pinnatifida, and S. missurica, is the sister to the rest of the Synthyris clade. Constraint topologies are used to test prior hypotheses of relationships and morphological similarities. Parametric bootstrapping is used to compare the likelihood values of the best trees obtained in searches under constraints to that of the best tree found without constraints. These results indicate that topologies in which a monophyletic Synthyris is the sister of Besseya are significantly worse than the best ML tree in which Synthyris is paraphyletic to Besseya. Similarly, forcing either the monophyly of all taxa that have deeply incised leaf margins or those that have reniform laminas and broadly rounded apices results in trees that are significantly worse than the best ML tree, in which leaf margin incision and reniform laminas are homoplastic. We propose a new classification for Synthyris that emphasizes monophyletic groups. The new combination Synthyris oblongifolia is proposed.