Vegetation changes of tropical Lizard Island (Great Barrier Reef World Heritage Area, Australia) over the last 8000 years are derived from palaeoenvironmental analysis of a 475 cm long sediment core. During early-Holocene sea-level rise, flooding of the continental shelf and thus isolation of Lizard Island, the pollen record shows the gradual establishment of a mangrove forest paralleled by contraction of the near-coastal palm and grass-dominated vegetation. Subsequently, mid-Holocene relative environmental stability supported a diverse, Rhizophora-dominated mangrove and open, mixed sclerophyll vegetation inland. Around 6000 years ago, a profound disturbance of the mangrove is recorded by a siliciclastic layer and we hypothesise that this deposit documents the impact of a storm or cyclone. Postevent environmental conditions were strongly altered with enhanced estuarine conditions supporting a Sonneratia and Bruguiera-dominated mangrove forest. During late-Holocene sea-level fall and stabilisation, progradation and contraction of the mangrove forest was paralleled by the expansion of a palm-dominated swamp. Freshwater taxa continued to dominate the record, however, a distinct disturbance signal from anthropogenic activity is recorded in the last century. Although Sonneratia dominated the post-event mangrove, late-Holocene environmental instability led to the extinction of this genus on the island. Local environmental changes in the freshwater swamp and rainforest also led to the loss of Arenga and Ilex from the island's ecosystems. Our record implies that long-term ecosystem and biodiversity change on Lizard Island is: (a) primarily reflected in the spatial extent of the island's vegetation communities and the species dominance within them and (b) driven by an interplay between climate, sea-level and potentially human activity. In addition, a short-term impact provoked the reconfiguration of the mangrove, potentially causing long-term ecosystem instability and thus impacting on mangrove biodiversity development on the Great Barrier Reef islands.