Marine ecosystems are under threat from many factors (e.g., harvesting, pollution, global climate change) that are degrading or destroying key habitats for fishes at an alarming rate. Historically marine habitats were broadly viewed as homogeneous structures over which fish travelled and lived. Now, however, marine stakeholders are realising habitats can range in quality, with huge consequences for fish biodiversity, replenishment and productivity. This has led to a rise in fish-habitat related studies over the last couple of decades, with a major focus on charismatic systems like coral reefs, seagrass and mangroves. Other habitats like tropical seaweed meadows or sponge gardens have not had adequate attention, until now. Using a multi-scale approach, my PhD explored the key predictors for patterns of marine fish community structure in these under-studied habitat types across tropical and temperate Australia. In this talk I will discuss the interplay between local habitat quality and seascape context, how an acute unseasonal habitat disturbance can have lasting effects on tropical fish communities, and what this means for future habitat-based approaches to conservation and management of diverse and productive seascapes.