Chemical investigations on the EtOAc extract of the cultures of Colletotrichum capsici afforded a novel indole–pyrazine alkaloid embodying a structurally unique C16N3-type skeleton, colletotrichumine A (1), together with five known steroids (2–6). Their structures were elucidated by spectroscopic analysis and that of 1 was further confirmed by a single-crystal X-ray diffraction method. The plausible biogenetic pathway of 1 was also discussed.