Serranids play important ecological roles in marine ecosystems as predators and support valuable fishing and tourism industries. They are known to occupy a range of tropical marine habitats including coral reefs, macroalgal meadows, seagrass beds and mangrove forests. Yet within these broad habitat types, some species prefer microhabitat structures such as tabular corals. We examined whether habitat condition could be an indicator for the distribution and abundance of serranids at Ningaloo reef across both coral back reef and macroalgal meadows over a six-year period (2013-2018). All species found during surveys were within coral back reef habitat, while only 6/17 species were found within macroalgal meadows. The dominant species found during surveys was Epinephelus rivulatus (78% of total) which predominantly occupied macroalgal meadows; the most abundant coral-affiliated species was E. fasciatus (10% of total). Inter-annual comparisons revealed shifts in abundance and size structure of species across the Ningaloo lagoon, particularly E. rivulatus within macroalgal meadows. Concurrent surveys of habitat condition suggest differences in habitat microstructure may be a key predictor for serranid abundance patterns. Understanding multi-scale patterns of fish-habitat association is essential for sustainable resource management to assess and forecast the consequences of changing habitat conditions for these important fishes.