In Hawaii, some of the most important commercial and recreational fishes comprise an assemblage of lutjanids and carangids called bottomfish. Despite their importance, we know little about their trophic ecology or where the mercury (Hg) that ultimately resides in their tissue originates. Here we investigated these topics, by analyzing muscle samples for mercury content, nitrogen, carbon, and amino acid specific nitrogen isotope ratios in six species distributed across different depths from the Northwestern Hawaiian Islands (NWHI) and the Main Hawaiian Islands (MHI). Fishes had different sources of nitrogen and carbon, with isotopic values suggesting benthic food sources for shallow nearshore species. High trophic position lutjanids that foraged in deeper water, benthic environments generally had higher Hg levels. Model results also suggested that benthic Hg methylation was an important source of Hg for shallow benthic feeders, while deepwater sources of mercury may be important for those with a diet that derives, at least in part, from the pelagic environment. Further, despite the lack of freshwater sources of Hg in the NWHI, statistical models explaining the variation in tissue Hg in the MHI and NWHI were nearly identical, suggesting freshwater Hg inputs were not a major source of Hg in fish tissue.