Eight compounds, including two new compounds, xishaxanthone A (1) and xishaxanthone B (2), and six known compounds (3–8), were isolated from the marine-derived fungus Penicillium sp. F28 and structurally characterized. Xishaxanthone A (1) is a new xanthone derivative which possesses a 1,7-dihydroxanthone skeleton with a methyl carboxylate group at C-8, a substitution pattern rarely encountered among xanthone natural products. The structure was determined by a combination of techniques including HR-ESI-MS (High-Resolution Electrospray Ionization Mass Spectrometry), NMR (Nuclear Magnetic Resonance), and ECD (Electronic Circular Dichroism) calculations. Furthermore, a hypothetical biosynthetic pathway for compound 1 is proposed.