The Mediterranean thermophilous woodlands were shaped by human activities for millenia, mainly for forage and fruits harvest. The recurring exchanges that followed between forests and cultivated areas have constituted a pivotal aspect in the process of Mediterranean fruit tree domestication. Since its domestication in the Middle-East around 6,000-4,000 years BP, the carob tree, Ceratonia siliqua L. (Leguminosae), has probably experienced extensive genetic and physiological modifications conducing to potential changes of a major compartment of its functioning: the microbiome. The carob tree is highly dependent of arbuscular mycorrhizal (AM) symbiosis, but some evidences tends to demonstrate bacterial endophytes as a second major symbiotic partner. In the framework of the international project DYNAMIC (Deciphering sYmbiotic Networks in cArob-based MedIterranean agro-eCosystems), high-throughput sequencing methods were applied to estimate several proxies of the carob tree-microbiome diversity and to correlate it to carob tree ecology and phylogeography at the Mediterranean scale. The results provide new insights into the characterization of a Mediterranean core and accessory carob tree-microbiome, highlighting geographical patterns, as well as the contribution of host genetic diversity, habitat and edaphic parameters. New avenues for reflexion regarding the relative role of history and habitat (cultivated vs wild) as drivers of tree-microbiome are also proposed. The conclusions open up promising perspectives for the development of more efficient strategies in conservation and agroecology based on tree-microbiome management.