The sooty blotch and flyspeck (SBFS) syndrome of apples and other fruits is caused by a complex consortium of epiphytic fungi that colonize the fruit cuticula. SBFS fungal strains isolated from apples were screened for growth inhibition of the phytopathogen Colletotrichum fioriniae in dual culture tests. Extracts of 11 isolates of SBFS fungi (Microcyclospora malicola, Microcyclospora pomicola, Microcyclospora tardicrescens, and Microcyclosporella mali) inhibited growth of the test strains and were studied for production of antibiotics. A strain of Microcyclospora tardicrescens strongly inhibited growth and was cultivated on a larger scale to characterize its secondary metabolites. Bioassay-guided fractionation and subsequent structure elucidation by spectroscopic and spectrometric methods (NMR, HRMS) yielded trichothecolone acetate (1) and its novel derivative (S)-7-hydroxytrichothecolone acetate (2) as active principles. Microcyclospora tardicrescens was thus identified as a producer of the hazardous trichothecene type mycotoxins for the first time, which should give reason to monitor these foodborne fungi more carefully in the future.