An ectomycorrhiza constitutes a mutualistic relationship between the mycelium of a fungus and the roots of a host plant. Truffles are important commercial ectomycorrhizal fungi, naturally present and abundant in Slovenia. The knowledge about their distribution and presence of associated fungi is scarce for natural sites but well defined for several truffles plantations established abroad.The study is the first example of the ectomycorrhiza community study from natural truffle sites in Slovenia.We aimed to analyse the ectomycorrhiza communities of natural Tuber aestivum sites from under two common ectomycorrhizal plant partners: hornbeam and oak. We have applied morphological and molecular approach in ectomycorrhiza identification to reveal the community structures. Tuber aestivum was observed in most soil samples in natural stands. Cenococum geophylum was present in all. Russula spp. only occurred with oaks while Tomentella spp, were more common with hornbeam. In comparison with truffle plantation, the community was different with only several in common, such as T. aestivum, Tarzetta sp. and some Tomentella species.