In recent years, the number of reports of Fusarium in association with hazelnut (Corylus avellana) has been increasing worldwide, related to both pathogenic aptitude and endophytic occurrence. However, the assessment of the real ecological role and relevance to plant health of these fungi has been impaired by uncertainty in species identification, deriving from both the evolving taxonomic structure of the genus and an inaccurate use of molecular markers. In this paper, the characterization of two hazelnut endophytic strains isolated in Poland is reported with reference to their secondary metabolite profiles and interactions with pests and pathogens. Our results are indicative of a possible role of these strains in defensive mutualism which could be related to the production of several bioactive compounds, especially cyclohexadepsipeptides of the enniatin family. At the same time, these biochemical properties create some concern for the possible mycotoxin contamination of hazelnut products.