A new 3H-oxepine-containing alkaloid, varioxepine A (1), characterized by a structurally unprecedented condensed 3,6,8-trioxabicyclo[3.2.1]octane motif, was isolated from the marine algal-derived endophytic fungus Paecilomyces variotii. Due to the low proton/carbon ratio, the unambiguous assignment of the planar structure and relative configuration was precluded by NMR experiments and solved by single crystal X-ray analysis. The absolute configuration was established by DFT conformational analysis and TDDFT-ECD calculations. Compound 1 inhibited plant pathogenic fungus Fusarium graminearum.