Botryosphaeriaceae are a diverse group of endophytic fungi colonizing the inner tissue of many woody species. As opportunist pathogens, they have been increasingly involved in diebacks worldwide. Nonetheless, the diversity of Botryosphaeriaceae, especially in asymptomatic plants, remains largely unknown. Using an innovative and mixed strategy of metabarcoding, this study aims to investigate the diversity of the fungal endophyte community, with a focus on Botryosphaeriaceae, which colonize grapevine and adjacent oak and pine trees in a French landscape. These data were used to test if the differentiation between hosts is more important than geographical effects for shaping the Botryosphaeriaceae communities and whether that similarity is higher between communities of grapevine and oak (both Angiosperms) than between oak and pine trees. We revealed a high level of diversity in Botryosphaeriaceae fungi, in both grapevines and forest trees, with a greater richness for grapevines. Contrasting results were obtained for the endophytic community, which was more diverse in forest trees. Our results support the hypothesis that host factors prevail on geographic effects to explain the diversity of Botryosphaeriaceae at the studied spatial scale. However, the features of the agroecosystem, such as management practices, were suggested to be more important than phylogeny to structure the fungal community. This highlights the importance of management practices for the microbiome of plants.