Two new prenylated indole alkaloids, 17-epinotoamides Q and M (1 and 2), and two new phenyl ether derivatives, cordyols D and E (9 and 13), together with 10 known compounds (3−8, 10−12, 14) were isolated from a marine-derived Aspergillus sp. fungus. Among them, 1/5 and 2/4 were pairs of epimers. The planar structures and absolute configurations of the new compounds were determined by extensive NMR spectroscopic data as well as CD spectra. The absolute configuration of 3 was confirmed by single-crystal X-ray diffraction analysis for the first time. All isolated metabolites (1−14) and eight synthetic phenyl ether derivatives (12a, 14a−14g) were evaluated for their antibacterial activities in vitro. The polybromide phenyl ether 14g showed pronounced antibacterial activity against Staphylococcus epidermidis with an MIC value of 0.556 μM, stronger than that of the positive control ciprofloxacin (MIC = 3.13 μM).