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