A chemical study on the n-BuOH-soluble fraction of the 95% EtOH extract of long-grain rice (Oryza sativa) fermented with the endophytic fungus Annulohypoxylon boveri var. microspora (BCRC 34012) has resulted in the isolation of one new natural azaphilone derivative, designated as annulohypoxyboverin (1) together with 12 known compounds, (3R,6R,7E)-3-hydroxy-4,7-megstigma-dien-9-one (2), α-tocopheryl quinone (3), isofraxidin (4), coumarin (5), cinnamic acid (6), a mixture of palmitic acid (7) and stearic acid (8), N-cis-feruloyltyramine (9), luteolin (10), kaempferol (11), kaempferitrin (12), and 4,5,4′,5′-tetrahydroxy-1,1′-binaphthyl (13). Annulohypoxyboverin (1) contains a dihydrobenzofuran-2,4-dione backbone, 1-hydroxyhexyl side chain, and one γ-lactone ring. Their structures were elucidated by spectroscopic analyses including 1D and 2D NMR experiments, and by HR-ESI-MS. The relative configuration of 1 was confirmed by NOESY experiment. Other known compounds were identified by comparing their spectral data with those of literature data.