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Ectomycorrhizal (ECM) fungi might play a major role in host plant establishment in polluted soils, by increasing plant nutrient supply and providing protection against pollutants. At the same time, host plants modify soil environment and allocate C substrates to ECM fungi, influencing the composition of associated ECM communities. These bi-directional relationships between host tree species and ECM communities are largely unexplored for Mediterranean ecosystems. Here, we characterized ECM fungal communities associated to Holm oak (Quercus ilex subsp. ballota) saplings in soils with a broad range of pH and trace element pollution, in Southern Spain. ECM species composition and relative abundance varied significantly among the studied sites. Soil abiotic conditions, such as pH and Ca, were influential in the ECM species distribution. Moreover, we found significant relationships between host tree traits and the ECM species distribution pattern. Specific leaf area (SLA) and the concentration of K, Mn, Ni and Cd in leaves were significantly correlated with the main trend of variation of ECM communities. Root chemical traits also correlated with the distribution of ECM species; in particular the concentration of macronutrients such as Ca, Mg and P, and trace elements such as Mn, Co, Cu and Cd. We explored causal models, through a structural equation modelling (SEM), to elucidate whether the influence of soil chemistry on host functional traits is mediated by changes in ECM diversity.