Mesophotic (30–150 m) reef fish assemblages in the ‘Au‘au Channel, between the Hawaiian Islands of Maui and Lanai, were compared visually with neighboring shallow (<30 m depth) reef fish assemblages for differences in structure. Between 2007 and 2011, approximately 7000 mesophotic and 4000 shallow reef fishes were identified, sized (standard length), and assigned to seven foraging guilds. The shallow water zone had more species than the mesophotic zone (99 vs 80, respectively). Mesophotic planktivores and two herbivore species were significantly larger than their shallow reef counterparts. Shallow reef fish assemblages had a higher Chao1 estimated species richness for herbivores and corallivores but not the other five foraging guilds. The differences between mesophotic and shallow fish assemblages indicate that both have unique communities of high conservation importance.