The factors influencing plant species diversity in secondary and ancient forests can differ. Apart from environmental variability caused by natural conditions, secondary forests are influenced by historical factors (previous human activity). However, the effect of historical factors on vegetation is not fully understood. Secondary forests that have developed in abandoned villages in the Doupovské hory mountains, Czech Republic, were surveyed and compared with ancient forests in an attempt to determine the effect of historical factors and separate it from that of natural gradients. The results show that secondary forests in abandoned villages form a unique type of vegetation that differs from ancient forests mainly in the presence of species indicating a high nutrient content and high pH of the soils. This indicates that the previous high nutrient input in the villages still influences the soils and causes the differences. Variability of village forests is influenced mainly by a gradient in the available phosphorus content of the soils, soil moisture (approximated by wetness index) and organic matter content. The pattern in the phosphorus content and pH indicate a different intensity of historical influence in the centre compared to the periphery of the villages. Vegetation variability is modified by former land-use and village structure. The effect of historical factors is relatively strong and cannot be explained by coincidental initial conditions.