This study surveyed several locations at depths between 50 and 140 m within the Au’au Channel, Hawaii to characterize the deep reef habitat and determine the depth distribution and relative abundance of the dominant, habitat forming megabenthic taxa. In the Au’au Channel, the depth distribution of megabenthic taxa exhibited a pattern of vertical zonation with relatively few taxa dominating each zone. Macroalgae particularly Halimeda spp. and to a lesser extent scleractinian corals Leptoseris spp. were dominant between 50 and 80 m; Leptoseris spp. were dominant between 80 and 90 m as macroalgae decreased in abundance; the invasive octocoral Carijoa riiseiwas dominant between 90 and 100 m primarily on rugose features; Antipathes spp. and Leptoseris spp. were dominant between 100 and 120 m on exposed fossil reef; and small wire corals were dominant between 120 and 140 m. In general, the percentage of live benthic cover decreased with depth, particularly below 90 m where a large majority of the area was uncolonized, soft substrata. The gradient of downwelling light intensity appears to play a major role in regulating the depth distribution of photosynthetic organisms, skilophilous organisms, and other benthic fauna, which compete for space with dominant photosynthetic species. The depth of the seasonal thermocline also appears to play an important role in limiting the distribution of tropical benthic species.