This study examined how habitat associations changed with ontogeny in the tiger tail seahorse Hippocampus comes Cantor, 1850, over four reef zones in a coral reef ecosystem. Hippocampus comes showed ontogenetic differences in their use of habitat at the scale of reef zones (macrohabitat) and holdfasts (microhabitat). Across reef zones, juvenile size classes (25–105 mm standard length, LS) were most abundant in wild macroalgal beds (Sargassum spp.) (55·7%), while adults (>105 mm LS) occupied both coral reefs (39·7%) and macroalgal beds (42·7%). Microhabitat use also varied with ontogeny. Juveniles generally used macroalgal holdfasts, while adults >135 mm LS used a greater diversity of specialized microhabitats that included branching sponges, branching corals and tall seagrass. Ontogenetic changes in habitat association, as well as size-related shifts in crypsis and aggregation, suggest that H. comes experiences fitness trade-offs that vary with size; juveniles may associate with habitat that reduces predation, while larger individuals may use distinct microhabitat in reef zones to optimize reproductive success. Results are discussed in the context of targeted exploitation, expanding artisanal mariculture, habitat damage from illegal fishing and reserve design.