With more than 200 cyprinid genera, Phoxinus is the only genus of minnows with a Holarctic distribution. With ten described species, the genus has received only minimal attention with respect to their phylogenetic relationships, despite the broad distribution of the genus, the brilliant coloration of most species, and the frequency of species in cold-water stream ecosystems. Once recognized in three genera (Phoxinus, Chrosomus, Pfrille), monophyly of the genus has been questioned through previous morphological and molecular investigations. Analyses of all North American species and the Eurasian species Phoxinus phoxinus from across its range using variation in complete sequences of cytochrome b, corroborate previous, less taxon-rich molecular studies using either nuclear or mitochondrial genes, that the genus is an unnatural assemblage. The revised taxonomy for the genus recognizes the North American genus Chrosomus inclusive of the monotypic subgenus Pfrille as the sister group to the remaining species of the subgenus Chrosomus and the whole clade as part of a lineage inclusive of the previously identified North American shiner and western clades. Given the limitations to the taxon sampling of this analysis, the Eurasian Phoxinus is a basal clade of leuciscine cyprinids. With the exception of C. neogaeus, the six North American species form three clades of paired sister species (C. erythrogaster + C. eos; C. cumberlandensis + C. saylori; C. oreas + C. tennesseensis). The phylogenetic relationships provided herein offer opportunities for detailed evolutionary studies of their ecologies, distributions, and behaviors.