Microketides A and B (1 and 2), a pair of new C-11 epimeric polyketides, were obtained from the gorgonian-derived fungus Microsphaeropsis sp. RA10-14 collected from the South China Sea. The absolute configurations of 1 and 2 were assigned by the modified Mosher's method, TDDFT-ECD, and NMR calculations. Compounds 1 and 2 were evaluated for antibacterial, antifungal, and growth inhibition of marine phytoplankton activities. Microketide A (1) exhibited promising inhibitory activity against Pseudomonas aeruginosa, Nocardia brasiliensis, Kocuria rhizophila, and Bacillus anthraci with the same MIC value as ciprofloxacin (0.19 μg/mL).