Two new chromones, phomochromone A and B (1 and 2), and one new natural cyclopentenone derivative, phomotenone (3), together with six known compounds, phomosines A-D (4-7), (1S,2S,4S)-trihydroxy-p-menthane (8), and 5-methylmellein (9), have been isolated from the endophytic fungus Phomopsis sp. through a bioassay-guided procedure. The structures of the new compounds were assigned on the basis of the 1 H and 13 C NMR spectra, DEPT, and 2D COSY, HMQC, HMBC, and NOESY experiments, supported by molecular modelling. The absolute configurations of compounds 1-3 were assigned by TD-DFT CD calculations and, surprisingly, the two related phomochromones A and B have an opposite configuration at C-2. Compounds 1-3 show good antifungal (Microbotryum violaceum), antibacterial (Escherichia coli, Bacillus megaterium), and antialgal (Chlorella fusca) activities. Compound 8 shows good antialgal and antibacterial activity.