Strawberries are susceptible to decay and destruction while being harvested and stored. This study had the following objectives: (1) the documentation of fungi and mycotoxin production associated with infected strawberry fruits; (2) the evaluation of the primary phytochemicals of Sargassum cinereum and Padina boergesenii by gas chromatography–mass spectrometry (GC–MS) and Fourier transform infrared (FT-IR) analysis to identify the active chemical composition of the seaweed extracts; and (3) the assessment of the antifungal activity of five extracts from brown seaweeds both in vitro and in vivo against fungal infections on fresh fruit under post-harvest conditions. The most common fungi were Aspergillus niger 14.36%, Botrytis cinerea 38.29%, and Mucor irregularis 16.88%. Padina boergesenii acetone extract had the highest in vitro antifungal activity. The methanol extracts of both S. cinereum and P. boergesenii were effective against the pathogenicity and aggressiveness (in vivo) on post-harvest strawberry fruits. B. cinerea could produce botrydial and dihydrobotrydial toxins with concentrations of 8.14 µg/mL and 4.26 µg/mL, respectively. A. niger could produce ochratoxin A with a concentration of 10.05 µg/mL. The present study demonstrates that the extracts of macroalgae S. cinereum and P. boergesenii contain secondary metabolites and antioxidants, indicating their potential utilization in antifungal applications.
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