Soil pollution by mercury (Hg) is a global problem that poses risks to natural ecosystems and to human health. Forests represent an important recipient of Hg deposition, however, so far, very little is known about the tree species identity effects on the distribution of Hg in forest soils and its accumulation in edible mushrooms. To clarify the effect on the two main Central-European commercial forest tree species, soil samples were collected from organic F+H horizons and from mineral soil depths of 0–2, 2–10, 10–20, and 20–30 cm in mature Norway spruce (Picea abies (L.) H. Karst.) and European beech (Fagus sylvatica L.) dominated stands. Mushroom samples of the Boletaceae family were also collected at each sampling site. The highest Hg contents were found in the F+H layer and were significantly higher in spruce- (mean 0.46 ± 0.03 mg/kg) than in beech- (mean 0.29 ± 0.10 mg/kg) dominated stands. The variation in Hg contents in F+H was best predicted by pH, the overall lower soil pH in strongly acidic spruce stands might induce Hg immobilization in the F+H layer to cause a decrease in the bioavailability of Hg for Xerocomellus chrysenteron (Bull.) Šutara. In mineral soil, the Hg contents did not differ significantly between the spruce- and beech-dominated stands. The Hg content strongly correlated with the S, N, and C contents only in mineral soil; at the depths of 2–10, 10–20, and 20–30 cm, significantly also with the silt vs. sand, Alo, and Feo contents. Studied mushroom species were not Hg-contaminated and, therefore, their consumption does not pose serious health risks regardless of the forest type. The results suggest that species-related soil chemistry and mineral associations, rather than different atmospheric Hg interception by spruce vs. beech, drive the vertical distribution and accumulation of Hg in forest soils.