The family Naucoridae (Heteroptera) has never been analyzed from a strict phylogenetic perspective in part because of the difficulty in assessing morphological attributes among constituent taxa. Thus, our goal is to combine molecular with morphological data to resolve relationships within this family. Phylogenetic relationships among subfamilies of Naucoridae were examined using a molecular dataset of one mitochondrial gene and one nuclear gene. Nine genera representing all five subfamilies were included in the analysis. Specimens preserved in 100% ethanol were used for DNA extraction, and other species of Nepomorpha were used as outgroups.