Two new quinazolinone diketopiperazine alkaloids, including versicomide E (2) and cottoquinazoline H (4), together with ten known compounds (1,3, and5–12) were isolated and identified fromAspergillus versicolorAS-212, an endozoic fungus associated with the deep-sea coralHemicoralliumcf.imperiale, which was collected from the Magellan Seamounts. Their chemical structures were determined by an extensive interpretation of the spectroscopic and X-ray crystallographic data as well as specific rotation calculation, ECD calculation, and comparison of their ECD spectra. The absolute configurations of (−)-isoversicomide A (1) and cottoquinazoline A (3) were not assigned in the literature reports and were solved in the present work by single-crystal X-ray diffraction analysis. In the antibacterial assays, compound3exhibited antibacterial activity against aquatic pathogenic bacteriaAeromonas hydrophiliawith an MIC value of 18.6 μM, while compounds4and8exhibited inhibitory effects againstVibrio harveyiandV. parahaemolyticuswith MIC values ranging from 9.0 to 18.1 μM.