Centuries of lead mining and smelting in Žerjav, N Slovenia resulted in elevated lead, cadmium and zinc concentrations in soil affecting plants, wildlife and human health. The remaining local flora served as basis for the selection of key species best suited for phytoremediation activities as they are already adapted to prevailing environmental conditions. Plant diversity and vegetation cover of mycorrhizal plant species by far exceeded our expectations, indicating the importance of root fungal colonisation for plant survival on the most polluted plots. Salix caprea is the only woody shrub species present in the vicinity of lead mine and smelter. Despite the severe metal pollution, root tips of S. caprea are colonised by diverse fungal morphotypes, with the black-coloured morphotypes being the most abundant. Element composition and spatial distribution of selected morphotypes were analysed using proton-induced X-ray emission (PIXE). Selection of indigenous plant-fungal symbionts is suggested as the most suitable management strategy for phytostabilisation. Their possible role in metal tolerance will be critically evaluated.