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Disturbances such as fires and grazing have major impacts on biodiversity. While it has been suggested that species richness is highest with intermediate levels of disturbance, currently there is no consensus due to an absence of data covering large temporal and spatial scales. We developed a new method to examine disturbance-diversity relationships (DDR) using sedimentary pollen data linked with species' disturbance ecology. We reconstructed disturbance and diversity dynamics in the region of the European temperate zone over the last 12,000 years and calculated DDR for 900-year sequential temporal windows. Disturbance frequency was highest in the early and late Holocene, while remaining low in the mid-Holocene. Diversity increased continuously from the start of the Holocene. Our results demonstrate that over the past 12,000 years DDR changed from hump-shaped into monotonic increasing pattern. While both highly disturbed and undisturbed sites were strongly impoverished in the early Holocene, as species migrated, biodiversity levels have subsequently affected disturbance regimes with highly disturbed sites now being the highest in species richness. Synthesis. Land-use changes in the last 4,000 years created an increasingly patchy landscape, allowing invasive species adapted to high-frequency disturbance to migrate across the landscape. The link between high diversity and disturbed areas is relatively recent and may anticipate even greater disturbance frequencies in future. Our findings also support a hypothesis that species migration, and the structure of the species pool critically determines the response of biota to external factors such as disturbance.