Identifying habitats important to vulnerable life stages of reef fish is an important goal for the effective design and management of Marine Protected Areas (MPAs). However, data on habitat requirements for most fish species are limited. Using a benthic habitat map that characterized reef habitats on the island of Hawaii , we examined ontogenetic patterns of habitat use by each of the life stages of endemic (i.e., Ctenochaetus strigosus; Ctenochaetus hawaiiensis), non-targeted species (i.e., Acanthurus nigrofuscus; Chromis agilis; Thallasoma duperrey; Paracirrhites arcatus) and targeted aquarium fish species (Zebrasoma flavescens; C. strigosus; C. hawaiiensis; Chaetodon multicinctus) in relation to the effectiveness of existing MPAs designed to replenish aquarium fishes targeted by the aquarium trade. Our study empirically demonstrates that many species shift habitats ontogenetically while others remained in the same habitats as they matured. And among those that shifted habitats, depending on species, adults shifted either to more structured (branching coral in mid-depth aggregate and boulder habitats in 5 to 11 m depths) or to less structured substrates (shallow turf-rich boulder habitats in 0 to 11 m depths). In addition, this study shows how the spatial characteristics of the MPA (i.e., reef size) may be important to reef fish assemblages and ultimately the effectiveness of MPAs to replenish protected ornamental fishes. It is therefore critically important that the management and future design of MPAs provide sufficient diversity and quantities of habitats for all life stages of managed species in order to ensure the replenishment necessary to satisfy their conservation needs and management goals.