Twelve new polyketides, including a naphthoquinone derivative, penithoketone (1), and 11 chromone derivatives, penithochromones A-L (2-12), together with three known compounds (13-15) were isolated from the deep-sea-derived fungus Penicillium thomii YPGA3. The structures of the metabolites were elucidated based on extensive analyses of the spectroscopic data, and the configuration of 1 was resolved by quantum chemical calculations of NMR shifts and ECD spectra and comparisons to experimental data. Compound 1, containing a naphthoquinone-derived moiety substituted with a butenolide unit, represents a new modified naphthoquinone skeleton. Interestingly, the 5,7-dioxygenated chromone derivatives 2-13 possessed different alkyl acid or alkyl ester side chain lengths, and those with side chain lengths of seven carbon atoms were discovered from nature for the first time. The metabolites were evaluated for their cytotoxicity against four cancer cell lines; compounds 1 and 15 were found to be active, with IC values ranging from 4.9 to 9.1 μM.