The genus Scouleria has three to five traditionally recognized species from Northeast Asia, western North America, and southern South America. While the genus is well defined by several morphological synapomorphies, species circumscriptions have varied, especially with respect to narrow versus broad concepts of S. aquatica. We used Maximum Likelihood and Bayesian phylogenetic analyses of ITS and the chloroplast loci ndhA, trnS-trnG, and rpL32-trnL to test species circumscriptions and to re-evaluate an earlier hypothesis of evolutionary relationships within the genus. Our results strongly support the recognition of S. marginata and S. patagonica as currently recognized based on geography and morphology. Phylogenetic patterns within S. aquatica sensu lato support the resurrection of two northeast Asian species, S. rschewinii and S. pulcherrima as distinct from North American S. aquatica sensu stricto. In addition, the recognition of the North American S. “species A” sensu Norris and Shevock (2004) as distinct from S. aquatica sensu stricto is supported. In all analyses, Drummondia prorepens (Drummondiaceae), rather than Tridontium tasmanicum (Scouleriaceae), was resolved as sister to Scouleria, thus providing support for the placement of Tridontium outside of Scouleriaceae.