To study the metabolites of the mangrove fungus Alternaria sp. R6, the compounds were isolated by silica gel and Sephadex LH-20 column chromatography. Their structures were characterized by spectroscopy. The antifungal activities were investigated using the broth tube dilution method. Ten compounds, including (4R,5R)-4,5-dihydroxy-3-methoxy-5-methyl-cyclohex-2-en-1-one(1), (4R, 5S,6R)-4,5,6-trihydroxy-3-methoxy-5-methyl-cyclohex-2-en-1-one (2), xylariacyclone B (3), (4S, 5S,6S)-5,6-epoxy-4-hydroxy-3-methoxy-5-methyl-cyclohex-2-en-1-one (4), LL-C10037α(5), 1- hydroxy-8-(hydroxymethyl)-6-methoxy-3-methyl-9H-xanthen-9-one (6), 8-hydroxy-6- methyl- 1- meth-oxycarbonyl-xanthen-9-one (7), 8-dimethoxy-1,6-dimethoxycarbonyl-xanthen-9-one(8), ergosterol and ergosterolperoxide, were isolated from the methanol extracts. Among them, the compounds 1, 2, 3, 4, 5, 6 and 8 were obtained from Alternaria sp. for the first time. The compounds 6 and 8 showed good inhibitory activity against Fusarium graminearum Schw. and Colletotrichum musae (Berk. & M. A. Curtis) Arx. While the compound 2 only showed good inhibitory activity against the latter.