We tested for depth-dependent vertical zonation in coral reef community structure with surveys conducted in 2013 at 10 m and 27 m depth oﬀ the islands of Moorea, Tahiti, Maiao, and Tetiaroa, which are distributed over ~3500 km2 of the tropical south Pacific. Benthic communities were censused using photoquadrats to obtain percentage cover, first by functional groups (scleractinians, macroalgae, and crustose coralline algae, algal turf, and bare space combined [CTB]), and second by genus for scleractinians and Millepora. Virtually every aspect of community structure diﬀered between the two depths, but the eﬀects were dependent on spatial scale of investigation. Interactive eﬀects of islands and depths determined the abundance of functional groups, as well as seven of eight common coral genera. On the two islands at which two sites were censused, the abundance of functional groups also diﬀered between sites, and was aﬀected by depth × site interactions. The spatially variable eﬀects of depth on community structure underscores the importance of context-specific synergy between biotic and abiotic factors in driving these patterns. Spatial scale-dependent vertical zonation also shows the potential for these eﬀects to be modulated by the changes that have aﬀected coral community structure on contemporary reefs over the last few decades.