Six new metabolites, namely cycloepoxylactone (1a), cycloepoxytriol A (2), cycloepoxytriol B (3) and phomolactones A–C (4–6), were isolated from two cultures of the ethyl acetate soluble fraction of the endophytic fungus Phomopsis sp. (internal strain no. 7233). Their structures were determined by means of spectroscopic data including HREIMS, 1H NMR, 13C NMR, and 2D NMR (HMQC, HMBC, and NOESY). The absolute configurations of 1a, 4 and 5 were determined by circular dichroism and comparison of solution CD spectra with TDDFT‐calculated ones. Preliminary studies showed that cycloepoxylactone (1a) has good antibacterial, antifungal, and algicidal activity against Bacillus megaterium, Microbotryum violaceum, and Chlorella fusca, respectively, whereas cycloepoxytriol B (3) has good algicidal activity against Chlorella fusca.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)