Five naphthoquinones including 4 compounds with new absolute configurations, (–)-2' S-trypethelone methyl ether (1), (–)-2' S-8-methoxytrypethelone methyl ether (2), (–)-(2' S,3' S)-4'-hydroxytrypethelone (3), and (–)-(2' S,3' R)-4'-hydroxy-8-methoxy trypethelone methyl ether (5), together with a known compound, (–)-2' S-trypethelone (4), were isolated from cultured mycobiont of Marcelaria cumingii. These compounds were structurally elucidated by high-resolution mass spectra, nuclear magnetic resonance, circular dichroism, optical rotation, and single-crystal X-ray analysis. The cytotoxicity against several cancer cell lines of the isolated compounds were tested. (–)-2' S-Trypethelone methyl ether (1) showed selective inhibition of HCT116 and A549 cell lines with half-maximal inhibitory concentration values of 0.32 ± 0.03 and 1.05 ± 0.12 µM, respectively. The binding conformation and molecular interactions including the effect of substituent modification were also revealed.