Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high‐throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft‐bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft‐bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.

Identifying organisms that play an important role in maintaining ecosystem function is a key aspect of resilience-based management. For Australia's Great Barrier Reef (GBR), we found that the recovery ability of shallow exposed fore-reefs is more than 14 times higher when tabular Acropora are present. The disproportionate role that tabular Acropora play appears to be driven by a combination of traits including high recruitment, high growth rate and, importantly, large maximum colony sizes. Despite this key role, tabular Acropora are highly sensitive to most pressures. We compile evidence suggesting that if tabular corals were to decline or disappear on the GBR, the potential for reef recovery on exposed fore-reefs would be considerably slowed. We then consider the merits of placing special emphasis on the protection of tabular Acropora within the management of the GBR. Importantly, we recognise that an analysis of costs and benefits of such recognition is vital before any change is implemented. Actions might include targeted crown-of-thorns starfish control, anchoring restrictions and protection for tabular corals on reefs identified as essential for their larval dispersal. In addition, targeted communications about the critical importance of these highly recognisable corals may boost community support and participation in their protection.

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