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In order to search for new lead compounds with anti-phytopathogenic bacterial activity, three pairs of new furanone derivatives, sclerotiorumins D–F (1–3), and eight known compounds (4–11) were isolated from the seaweed-derived fungus, Aspergillus sp. D40, fermented with potato dextrose seawater (PDW) medium. Their structures were determined using comprehensive spectroscopic analyzes including HRESIMS, 1D and 2D NMR data. Compounds 1–4 and 9 existed as inseparable mixtures of a pair of epimers. Penicillic acid (7) exhibited clear antibacterial activity against Ralstonia solanacearum and several other plant pathogenic bacteria with IC50 values ranging from 11.6 to 58.2 μg/mL.