Marine fungi associated with algae are promising producers of bioactive secondary metabolites. In this study, a Penicillium sp. was isolated from the brown alga Padina sp. (South China Sea, Vietnam) and identified using morphological and molecular genetic methods. The fungus was cultured, and its metabolites were extracted with ethyl acetate and purified by column chromatography and HPLC, yielding three compounds: 4-hydroxy-3,6-dimethyl-2-pyrone (1), 4-methoxyisoquinolin-1(2H)-one (2), and N,N-diethyl-3-methylbenzamide (3). Compound 1, a known terrestrial fungal metabolite, had its crystal structure determined for the first time. Compounds 2 and 3, previously known as synthetic derivatives, were isolated from a natural source for the first time. Cytotoxicity assays against murine splenocytes and erythrocytes showed no activity for 1–3 at concentrations up to 100 μM. Compound 1 exhibited weak radical-scavenging activity against diphenylpicrylhydrazide.