Chemical investigation of the ethyl acetate extract of an endophytic fungus, Alternaria brassicae JS959 derived from a halophyte, Vitex rotundifolia, led to the isolation of a new chromone, (2'S)-2-(2-acetoxypropyl)-7-hydroxy-5-methylchromone (1), along with sixteen known compounds: a chromone (2), twelve benzopyranones (3-14) and three perylenequinones (15-17). The chemical structures of the isolated compounds were identified by extensive spectroscopic data analysis including 1D, 2D NMR, HRESIMS, and optical rotation. Of these compounds, 1 and 2 showed inhibitory activity on Cu2+‒induced low density lipoprotein (LDL) and high density lipoprotein (HDL) oxidation in human blood plasma. The results suggest that metabolites of endophytic microbes could provide the basis for developing treatments for heart disease.