Shallow inshore coral reefs are under threat from a changing climate reducing the habitats condition; however, they form a component of a broader seascape with other habitats. Each of these habitats support distinct fish communities, yet it remains unknown how functionally similar these are and whether these habitats could support the functional composition of shallow reefs. We surveyed fish in five habitats (island seagrass, island mangroves, back-reef, and shallow and deep reefs) at 145 sites within reef island seascapes four times and used alpha and beta functional diversity to identify potential refugia from shallow reefs for fish and assessed where in the seascape community similarity is maximised. Shallow reefs had similar alpha functional diversity and low beta functional dissimilarity with island mangroves, back-reefs and deep reefs. Island mangroves with larger reefs nearby, back-reefs with low seagrass extent and seascape diversity nearby, and deep reefs further from seagrass supported functionally similar communities to shallow reefs. Identifying suitable locations where fish can move under climate change is crucial for the long-term management and functioning of coral reefs. Yet, there are locations within the seascape supporting functional dissimilar communities, with reduced competition for niche space, which reef fish can occupy in the future.