Earth’s ecological assemblages are rapidly being driven towards unprecedented, novel states. Novel communities are often defined by their unexpected species compositions; under anthropogenic activities, ecologists and managers are increasingly interested in how this novelty may extend beyond taxonomic turnover to affect the functional composition of communities. We know little about ecological novelty in our oceans across both taxonomic and functional community classifications, despite evidence that modern marine communities are experiencing greater rates and magnitudes of change than both modern terrestrial ecosystems and historical marine ecosystems. Here, we provide a quantitative assessment of taxonomic and functional ecological novelty in coral assemblages along the east Australian coast over the past 1,500 years, capturing changes in the composition of coral taxa and traits. Taxonomic novel communities emerged more frequently and often independently of substantial trait compositional change, while functional novelty commonly emerged alongside significant genus turnover. Novel coral communities themselves were rare, context-dependent, and associated with relative abundance shifts of common taxa. Though preliminary, our functional community classifications complement classical taxonomic methods to uncover a history of ecological change in east Australian coral communities, helping provide important context for their present states and inform future responses under ongoing and intensifying human-driven change.