Abstract: Multiple habitats in a tropical seascape are increasingly recognized as interconnected to one another. Mangroves, seagrass beds, and macroaglal beds are important components of a tropical seascape, and although they are unique and important in their own right, they also contribute to patterns and processes on coral reefs. In my PhD, I explore how non-reef habitats affect coral reef fishes in a highly connected seascape on Siquijor Island in the Philippines. Combining traditional reef fish and benthic habitat surveys with habitat mapping and spatial analysis of the seascape, I explore how fishes respond to habitat across multiple spatial scales. Firstly, I examine the relative importance of within-patch benthic habitat of coral reefs and adjacent non-reef habitats in the seascape on coral reef fish populations and assemblages. I then use DNA analysis to identify juvenile parrotfish species using non-reef habitats to investigate potential ontogenetic shifts. Finally, I utilise stable isotope analysis to explore diet and habitat use for important ‘herbivorous’ coral reef fish species (parrotfishes and rabbitfishes) to understand their diet and habitat use patterns. I found that coral reef fishes are influenced by non-reef habitats in the surrounding seascape, and that habitat within 500-m of coral reefs should be incorporated in species-habitat relationships. DNA analysis revealed an increase in non-reef habitat use for juvenile parrotfishes, and identified macroalgal habitat as a potentially important nursery habitat. I also found that habitat availability may be altering how species use non-reef habitats. My research highlights the importance of considering fish-habitat relationships at larger spatial scales, and underscores the importance of including non-reef habitats in future research.