Mesophotic Coral Ecosystems (MCEs; 30 150 m deep reefs) may provide natural refuges for fisheries targeted species by virtue of their depth. We surveyed shallow reefs and MCEs around Cozumel, Mexico including sites inside and outside a protected area. Our results suggest fish communities shifts across the depth gradient are affected by protection levels. Greater overall fish biomass, with larger body lengths of commercially valuable fish, were found in the shallows within the marine park than in areas with no protection. On MCEs however, fish biomass and commercially valuable fish body lengths were similar regardless of protection; implying deep reef areas act as natural refuges. These findings highlight the need to integrate fish populations on MCEs into current reef fisheries management plans.