Two novel benzoquinone metabolites, 2-chloro-5-methoxy-3-methylcyclohexa-2,5-diene-1,4-dione ( 1) and xylariaquinone A ( 2) together with two known compounds were isolated from an endophytic fungus, Xylaria sp. Their structures were assigned by analysis of spectroscopic data, and the structures of 1 and 3 were also confirmed by single-crystal X-ray data. Compounds 1 and 2 showed in vitro activity against Plasmodium falciparum, K1 strain, with IC 50 values of 1.84 and 6.68 microM and cytotoxicity against African green monkey kidney fibroblasts (Vero cells) with IC 50 values of 1.35 and >184 microM, respectively.