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Two novel fungal polyketides, phometides A (1) and B (2), together with four known compounds (3–6), were isolated from the endophytic fungus Phoma sp. YUD17001 obtained from Gastrodia elata Blume. The structures were elucidated based on spectroscopic analyses, X-ray crystal diffraction, and time-dependent density functional theory/electronic circular dichroism (TDDFT/ECD) calculations. Structurally, phometide A (1) represented the first example of C 12 polyketide characterized by an unusual tetrahydrobenzofuran-3(2 H)-one core with an α , β -unsaturated ketone functionality, while phometide B (2) was an unprecedented molecule containing a 2-pentylcycloheptan-1-one scaffold. In an antimicrobial activity assay, phometide A (1) exhibited significant inhibitory activity against Staphylococcus aureus with MIC value of 4 μg/mL. Phometide B (2) showed moderate antifungal activity against Candida albicans with an MIC value of 16 μg/mL. Furthermore, compounds 1 and 2 were evaluated for their acetylcholinesterase inhibitory and cytotoxic activities. [Display omitted] • Two novel fungal polyketides were identified from the endophytic fungus Phoma sp. YUD17001. • Phometide A possess an unusual tetrahydrobenzofuran-3(2 H)-one functionality. • Phometide B is a novel polyketone containing a 2-pentylcycloheptan-1-one scaffold. • Phometides A and B demonstrated antimicrobial activity against S. aureus and C. albicans , respectively. [ABSTRACT FROM AUTHOR]