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By treating with histone-deacetylase inhibitor valproate sodium, three new heterdimeric tetrahydroxanthone–chromanone lactones chrysoxanthones A–C (1–3), along with 17 known compounds were isolated from a sponge-associated Penicillium chrysogenum HLS111. The planar structures of chrysoxanthones A–C were elucidated by means of spectroscopic analyses, including MS, 1D, and 2D NMR. Their absolute configurations were established by electronic circular dichroism (ECD) calculations. Chrysoxanthones A–C exhibited moderate antibacterial activities against Bacillus subtilis with minimum inhibitory concentration (MIC) values of 5–10 μg/mL.