Microbial endophytes are well known to protect host plants against pathogens, thus representing a promising strategy for the control of Xylella fastidiosa in olive trees. Although their high potential for being used as biocontrol agents, there are pending questions regarding to which extent endophytes enhance plant defences. For example, how microbial fluctuations in the endosphere correlate to plant health? Also, what are the traits that enable endophytes to protect the host plant from pathogens? A better understanding of these questions will assist in the design of new strategies for the control of X. fastidiosa. In this study, the xylem microbiome of two olive cultivars with different susceptibilities to X. fastidiosa (i.e. cvs. FS17 is resistant while cv. Kalamata is susceptible) and with different amounts of X. fastidiosa in their xylem vessels, were analysed and compared. Twigs of three cultivars growing in the same orchard in the outbreak area in Italy were collected, and used to assess X. fastidiosa infection status by qPCR and xylem-associated microbiome. After DNA extraction from xylem tissue, both bacterial and fungal communities were assessed through sequencing (Illumina MiSeq) of the 16S rRNA V4 amplicons (pair primers 515f/806rB) and ITS1 -spanning amplicons (pair primers ITS1F-ITS2), respectively. A total of 86 bacterial and 310 fungal OTUs inhabiting the xylem sap of the three cultivars were identified. There are bacterial and fungal families that are preferential colonizers and the OTUs distribution within these families differs among the olive tree cultivars. Xylem core microbial community of the cv. Kalamata was dominated by Enterobacteriaceae (within bacteria) and Cucurbitariaceae / Herpotrichiellaceae (within fungi), while the xylem of cv. FS17 was colonized mostly by Sphingomonadaceae (within bacteria) and Teratosphaeriaceae (within fungi). A distinct core communities of bacteria and fungi associated with each infection status of the olive trees (highly or poorly infected by X. fastidiosa) was also identified. The most parsimonious assumption is that the core microbiome comprises microorganism with relevance to olive tree health. The potential role of these microorganisms in conferring olive tree protection against X. fastidiosa should be studied in the future.