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The Bohemian Forest Ecosystem encompasses various wildlife management systems. Two large, contiguous national parks (one in Germany and one in the Czech Republic) form the centre of the area, are surrounded by private hunting grounds, and hunting regulations in each country differ. Here we aimed at unravelling the influence of management-related and environmental factors on the distribution of red deer (Cervus elaphus) and roe deer (Capreolus capreolus) in this ecosystem. We used the standing crop method based on counts of pellet groups, with point counts every 100 m along 218 randomly distributed transects. Our analysis, which accounted for overdispersion as well as zero inflation and spatial autocorrelation, corroborated the view that both human management and the physical and biological environment drive ungulate distribution in mountainous areas in Central Europe. In contrast to our expectations, protection by national parks was the least important variable for red deer and the third important out of four variables for roe deer; protection negatively influenced roe deer distribution in both parks and positively influenced red deer distribution in Germany. Country was the most influential variable for both red and roe deer, with higher counts of pellet groups in the Czech Republic than in Germany. Elevation, which indicates increasing environmental harshness, was the second most important variable for both species. Forest cover was the least important variable for roe deer and the third important variable for red deer; the relationship for roe deer was positive and linear, and optimal forest cover for red deer was about 70% within a 500 m radius. Our results have direct implications for the future conservation management of deer in protected areas in Central Europe and show in particular that large non-intervention zones may not cause agglomerations of deer that could lead to conflicts along the border of protected, mountainous areas.