A search for endophytes in Castanea sativa Miller (Fagales: Fagaceae) grafting scions showed that a latent pathogenic fungus Gnomoniopsis smithogilvyi (Diaporthales: Gnomoniaceae) was present as the major component of the endophytic flora. Initially, the goal of this study was to develop a biological control method of Cryphonectria parasitica (Diaporthales: Valsaceae), the chestnut blight agent, by soaking chestnut scions before grafting in antagonists suspension. However, the healthy chestnut material used in in vitro and glasshouse experiments turned out to be naturally infected by a pathogen. At first view, the symptoms looked very similar to those caused by C. parasitica but some differences were noticed. DNA sequencing and application of Koch’s postulates revealed that G. smithogilvyi was the agent responsible of those symptoms. Preventive biocontrol experiments were carried out with chestnut tree scions soaked overnight in a liquid suspension of Bacillus amyloliquefaciens (Bacillales: Bacillaceae). This bacterium was then frequently found in the lower parts of scions (CF of 100% between 3.1 and 6 cm) and up to a height of 18 cm. It was observed that when B. amyloliquefaciens was present, the endophytic and opportunistic pathogenic fungus G. smithogil­vyi was not present. Conversely, the parts not colonized by the bacteria were always naturally infected by the endophytic fungus. This would indicate that the endophytic behavior of B. amyloliquefaciens inhibited the growth of G. smithogilvyi and reduced its presence in scions. A similar experiment, carried out with the Trichoderma atroviride (Hypocreales: Hypocreaceae), led to similar observations. Trichoderma atroviride was frequently isolated in the lower parts of scions (CF of 100% until 6 cm) and up to a height of 27 cm. Inoc­ulating B. amyloliquefaciens and T. atroviride as part of a preventive biocontrol treatment would allow these biological control agents to colonize the plant as endophytes and prevent the development of G. smithogilvyi.