Mitochondrial (cyt b and ND2) and nuclear gene (S7 intron 1) sequences were generated to evaluate phylogenetic relationships and validity of the monotypic minnow genus Opsopoeodus. Parsimony and Bayesian phylogenetic analyses of the mitochondrial markers resulted in largely unresolved relationships among ingroup taxa. Relationships recovered from the nuclear intron were well resolved and consistent with previously published morphological, chromosomal, and behavioral data that supported the recognition of Opsopoeodus as a genus. Although mitochondrial genes recovered species as strongly supported clades, they provided limited resolution of relationships among ingroup species and genera and showed high levels of saturation at inter-genus levels of divergence. These findings re-emphasize the importance of considering multiple datasets in making taxonomic decisions and caution against use of single gene trees alone.