Alnus glutinosa (black alder) is a mycorrhizal pioneer tree species with tolerance to high concentrations of salt in the soil and can therefore be considered to be an important tree for the regeneration of forests areas devastated by excessive salt. However, there is still a lack of information about the ectomycorrhizal fungi (EMF) associated with mature individuals of A. glutinosa growing in natural saline conditions. The main objective of this study was to test the effect of soil salinity and other physicochemical parameters on root tips colonized by EMF, as well as on the species richness and diversity of an EMF community associated with A. glutinosa growing in natural conditions. We identified a significant effect of soil salinity (expressed as electrical conductivity: ECe and EC1:5) on fungal taxa but not on the total level of EM fungal colonization on roots. Increasing soil salinity promoted dark-coloured EMF belonging to the order Thelephorales (Tomentella sp. and Thelephora sp.). These fungi are also commonly found in soils polluted with heavy-metal. The ability of these fungi to grow in contaminated soil may be due to the presence of melanine, a natural dark pigment and common wall component of the Thelephoraceae that is known to act as a protective interface between fungal metabolism and biotic and abiotic environmental stressors. Moreover, increased colonization of fungi belonging to the class of Leotiomycetes and Sordiomycetes, known as endophytic fungal species, was observed at the test sites, that contained a larger content of total phosphorus. This observation confirms the ability of commonly known endophytic fungi to form ectomycorrhizal structures on the roots of A. glutinosa under saline stress conditions.Electronic supplementary materialThe online version of this article (10.1007/s13199-017-0512-5) contains supplementary material, which is available to authorized users.