Long-term lead mining and smelting activities in Žerjav area has resulted in global metal pollution and degradation of environment. Associations of plants with fungal endophytes may alleviate stress and improve survival of plants in extreme environments. The root samples of three different tree species (goat willow, silver birch and scots pine) and their rhizosphere soils were collected at two different sampling sites (P2 and P3). The total organic content, plant accesible phosphorus, the total metal concentration and pH were measured on soil samples. Colonisation with ectomycorrhizal (EM), arbuscular mycorrhizal (AM) and dark septate endophytes (DSE) was evaluated. EM colonisation dominated in all tree species at both sampling sites. Positive correlation between the level of DSE colonisation and increased soil metal concentration was confirmed. DNA was isolated from different EM morphotypes. Fungal symbionts were identified with molecular methods (PCR, sequencing). Fungi from family Sordariaceae were the most abudant in goat willow, Thelephoraceae dominated in silver birch and Pyronemataceae were the most common in scots pine. The results show that tree species is more important factor determining mycorrhizal colonisation and fungal community structure than the sampling site (degree of pollution).