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In 1927, the first pollen diagram was published from the Bohemian/Bavarian Forest region of Central Europe, providing one of the first qualitative views of the long-term vegetation development in the region. Since then significant methodological advances in quantitative approaches such as pollen influx and pollen-based vegetation models (e.g., Landscape Reconstruction Algorithm, LRA) have contributed to enhance our understanding of temporal and spatial ecology. These types of quantitative reconstructions are fundamental for conservation and restoration ecology because they provide long-term perspectives on ecosystem functioning. In the Bohemian/Bavarian Forests, forest managers have a goal to restore the original forest composition at mid-elevation forests, yet they rely on natural potential vegetation maps that do not take into account long-term vegetation dynamics. Here we reconstruct the Holocene history of forest composition and discuss the implications the LRA has for regional forest management and conservation. Two newly analyzed pollen records from Prášilské jezero and Rachelsee were compared to 10 regional peat bogs/mires and two other regional lakes to reconstruct total land-cover abundance at both the regional- and local-scales. The results demonstrate that spruce has been the dominant canopy cover across the region for the past 9,000 years at both high- (>900 m) and mid-elevations (>700–900 m). At the regional-scale inferred from lake records, spruce has comprised an average of ~50% of the total forest canopy; whereas at the more local-scale at mid-elevations, spruce formed ~59%. Beech established ~6,000 cal. years BP while fir established later around 5,500 cal. years BP. Beech and fir growing at mid-elevations reached a maximum land-cover abundance of 24% and 13% roughly 1,000 years ago. Over the past 500 years spruce has comprised ~47% land-cover, while beech and fir comprised ~8% and