Aim: Marine reef habitats are typically defined subjectively. We provide a continental-scale assessment of dominant reef habitats through analysis of macroalgae and sessile animal taxa at sites distributed around Australia. Relationships between reef habitats and environmental and anthropogenic factors are assessed, and potential changes in the future distribution and persistence of habitats are considered. Location: Shallow rocky and coral reefs around the Australian coast. Methods: Cover of 38 sessile biota functional groups was recorded in diver-based surveys using quadrats at 1,299 sites. Classification analyses based on the functional groups were used to identify an unambiguous set of ‘biogenic habitat types’. Random forest and distance-based linear modelling were used to investigate correlations between these habitats and environmental and anthropogenic variables. Results: Cluster analyses revealed tropical and temperate ‘realms’ in benthic substratum composition, each with finer-scale habitats: four for the temperate realm (canopy algae, barren, epiphytic algae–understorey and turf) and five for the tropical realm (coral, coral–bacterial mat, turf–coral, calcified algae–coral and foliose algae). Habitats were correlated with different sets of environmental and anthropogenic conditions, with key associations in the temperate realm between mean sea temperature and canopy-forming algae (negative) and barren habitat (positive). Variation in sea temperature was also an important correlate in the tropical realm. Main conclusions: Quantitative delineation of inshore reef habitats at a continental scale identifies many of the same habitat types traditionally recognized through subjective methods. Importantly, many biogenic reef habitats were closely related to environmental parameters and anthropogenic variables that are predicted to change. Consequently, habitats have differing likelihood of persistence. Structurally complex habitats in the temperate realm are at greater risk than more ‘two-dimensional’ habitats (e.g., canopy-forming versus turfing algae). In the tropical realm, offshore and coastal habitats differed greatly, highlighting the importance of large-scale oceanic conditions in shaping biogenic structure.