The impact of plant species on the soil microbial communities and the physico-chemical characteristics of the soil begins to be well documented especially for non-perennial plants. However, our understanding of the diversity and structure of the tree-associated microbial communities as well as the of tree species effect remains limited. Here, we investigated the archaeal, bacterial and fungal communities in replicate soil samples, using16S rRNA,18S rRNA and fungal ITS sequences, in the long term experimental site of Breuil-Chenue. We showed significant difference in abundance, composition and structure of the microbial communities associated to two contrasted tree species, Fagus sativa and Picea abies developed on the same soil. Our results highlighted a strong host effect on the soil microbial communities, with a stronger effect on the fungal communities. Although the pyrosequencing approach showed a limited rhizosphere effect, quantitative PCR revealed a significant enrichment of specific bacterial genera known for their ability to weather minerals in the tree root vicinity. At last, co-occurrence analysis revealed very different networks below the two tree species, suggesting a modification of the structure and abundance of the microbial communities, but also modification of the interactions established between microorganisms. In all the microbial communities considered we observed a host effect with variable intensity, suggesting that the tree host shapes its soil microbiome.