Complete mitochondrial DNA cytochrome b gene sequences from 56 specimens representing all 12 species of Lepomis were used to examine phylogenetic relationships within the genus. Results supported the monophyly of Lepomis and all previously recognized subgenera, except Eupomotis, but there was no support for previously proposed relationships among subgenera. Seven species were recovered as monophyletic lineages, while five species (L. auritus, L. macrochirus, L. marginatus, L. miniatus, and L. symmetricus) were recovered as either poly- or paraphyletic or were placed as parts of unresolved polytomies with other species. Parametric bootstrapping tests rejected monophyly for only two of the five species (L. auritus and L. symmetricus). Without additional data, including increased geographic sampling and a comparable nuclear gene phylogeny, it is not possible to determine whether the failure to support monophyly for these two species reflects the presence of cryptic species or results from hybridization.