<jats:title>Abstract</jats:title><jats:p>Three new indole diketopiperazine alkaloids, 11‐methylneoechinulin E and variecolorin M, and (+)‐variecolorin G, along with 12 known analogs, were isolated from a soft coral‐associated epiphytic fungus <jats:italic>Aspergillus</jats:italic> sp. EGF 15‐0‐3. The structures of the new compounds were unambiguously established by extensive spectroscopic analyses including HR‐ESI‐MS, 1D and 2D NMR spectroscopy and optical rotation measurements. The absolute configurations of (+)‐ and (−)‐variecolorin G were determined by experimental and quantum‐chemical ECD investigations and single‐crystal X‐ray diffraction analysis. Variecolorin G is a pair of enantiomeric mixtures with a ratio of 1 : 2. Moreover, (+)‐neoechinulin A is firstly reported as a natural product. The cytotoxic activities of all the isolated compounds against NCI‐H1975 gefitinib resistance (NCI‐H1975/GR) cell lines were preliminarily evaluated by MTT method.