A survey of both ectomycorrhizal (ECM) root tips and fruiting bodies of 1 ECM fungi was carried out during a four-year period (2009–2012) in two similar forest stands in central Italy, previously investigated in detail being habitats of the Italian white truffle Tuber magnatum Pico. This research is one of the few conducted in mixed forest stands and, for the first time, it took into account the cryptic fungi (corticiaceous, hypogeous and sclerotia). This survey led to an exhaustive description of the ECM community by integrating all the 197 taxa recorded (147 species as fruiting bodies, 65 as ectomycorrhizas and 15 overlapping taxa recorded by both systems), and it also revealed a discrepancy between the results obtained using these two different approaches. In fact, a prevalence of Russulaceae, Inocybaceae and Cortinariaceae resulted from fruiting body observations, whereas Thelephoraceae and Sebacinaceae dominated the ECM root tips. This result suggests a probable flaw in the sampling methodology. There may be several causes of this phenomenon; including the different nutritional strategies of ectomycorrhizal fungi and their seasonal turnover. Some species that could be candidates as bioindicators of T. magnatum habitat in mixed forest were identified.