Bioassay-guided fractionation of the crude extract from Penicillium commune SD-118, a fungus obtained from a deep-sea sediment sample, resulted in the isolation of a known antibacterial compound, xanthocillin X (1), and 14 other known compounds comprising three steroids (2-4), two ceramides (5 and 6), six aromatic compounds (7-12), and three alkaloids (13-15). Xanthocillin X (1) was isolated for the first time from a marine fungus. In the bioassay, xanthocillin X (1) displayed remarkable antimicrobial activity against Staphylococcus aureus and Escherichia coli, and significant cytotoxicity against MCF-7, HepG2, H460, Hela, Du145, and MDA-MB-231 cell lines. Meleagrin (15) exhibited cytotoxicity against HepG2, Hela, Du145, and MDA-MB-231 cell lines. This is the first report of the cytotoxicity of xanthocillin X (1).