Biome boundaries are expected to be sensitive to changes in climate and disturbance, because it is here that ecological communities are at environmental, ecological or disturbance limits. Using palaeoecology to study ecosystem dynamics at biome boundaries provides opportunities for understanding ecosystem resilience or sensitivity at ecologically meaningful timescales, and under varying climatic and disturbance conditions.The fynbos biome is a megadiverse Mediterranean type shrubland, found only in South Africa, that is threatened by climate change, land-use change and invasion by alien species. We used palaeoecological records from the semi-arid and mesic boundaries of the fynbos biome to test hypotheses regarding ecosystem resilience over timescales of centuries to millennia. We hypothesised that fynbos would expand at its mesic boundary at the expense of afrotemperate forest under drier and / or more fire prone conditions. In contrast, we hypothesised that at the semi-arid boundary, fynbos would expand at the expense of succulent karoo under wetter and cooler and / or more fire-prone conditions. Contrary to our expectations, the fossil pollen record at both biome boundaries showed remarkable stability at centennial - millennial timescales. To explain our results, we generated new hypotheses exploring possible mechanisms that might confer resilience.At the mesic (temperate) boundary, we suggest that decreased seasonality of rainfall during drier phases favoured fire and fynbos persistence, while in wetter periods, increased seasonality of rainfall resulted in enhanced summer drought stress, inhibiting forest expansion. At this boundary, internal reorganisation from grassy to proteoid fynbos states conferred resilience through resistance. At the succulent karoo boundary, we suggest that increased aridity was offset by less seasonality of rainfall, which enhanced biomass and allowed fire to persist, favouring persistence of fynbos. At this boundary, fynbos sensu stricto retreated during arid phases but recovered during climate amelioration, consistent with resilience through recovery. In both cases, this mega-diverse, disturbance-adapted flora provided a range of traits that enabled fynbos to persist despite environmental perturbation. Our findings agree with general observations that for ecosystems in regions of ample resource availability (i.e. at the mesic boundary), biotic interactions and disturbance tend to become more important in ecosystem dynamics, whereas in regions of scarce resources (in this case water scarcity at the semi-arid boundary) abiotic stress is more important. Our findings contribute to debates over the mechanisms that confer resistance and resilience to environmental change. Understanding and conserving the processes and mechanisms underpinning its resilience will be critical to effective conservation planning.