Fungi from the genus Diaporthe have been reported as plant pathogens, endophytes, and saprophytes on a wide range of host plants worldwide. Their precise identification is problematic since many Diaporthe species can colonize a single host plant, whereas the same Diaporthe species can inhabit many hosts. Recently, Diaporthe has been proven to be a rich source of bioactive secondary metabolites. In our initial study, 40 Diaporthe isolates were analyzed for their metabolite production. A total of 153 compounds were identified based on their spectroscopic properties—Ultraviolet-visible and mass spectrometry. From these, 43 fungal metabolites were recognized as potential chemotaxonomic markers, mostly belonging to the drimane sesquiterpenoid-phthalide hybrid class. This group included mainly phytotoxic compounds such as cyclopaldic acid, altiloxin A, B, and their derivatives. To the best of our knowledge, this is the first report on the metabolomic studies on Diaporthe eres species complex from fruit trees in the South-Eastern Poland. The results from our study may provide the basis for the future research on the isolation of identified metabolites and on their bioactive potential for agricultural applications as biopesticides or biofertilizers.