Cytochrome b sequences (1140 bp) from 16 species considered to be members of subgenus Notropis and several outgroup taxa were analyzed phylogenetically. Phylogenetic analysis of cytochrome b was sensitive to sampling of outgroup taxa, probably resulting from substitutional rate heterogeneity among outgroups. Maximum-likelihood analysis was more robust to these effects as compared to maximum parsimony. Both maximum parsimony and maximum-likelihood analysis supported removal of Notropis candidus and Notropis shumardi from subgenus Notropis. Monophyly of the 14 remaining species was supported by the maximum likelihood analysis. Regardless of the method of analysis or use of outgroup taxa, phylogenetic analysis of cytochrome b indicated strong support for the following hypothesis of relationships: ((Notropis rubellus, Notropis suttkusi), (Notropis amoenus, Notropis stilbius, ((Notropis atherinoides, Notropis oxyrhynchus), (Notropis amabilis, Notropis jemezanus)))). This phylogenetic hypothesis implies that morphological characters associated with increased olfaction were derived independently among members of subgenus Notropis, perhaps in response to life in more turbid habitats.