AbstractThree new prenylated indole alkaloids, including two β‐carbolines, penipalines A and B (1 and 2, resp.), and one indole carbaldehyde derivative, penipaline C (3), as well as two known indole derived analogs, 4 and 5, were isolated from the deep‐sea‐sediment derived fungus Penicillium paneum SD‐44 cultured in a 500‐l bioreactor. The structures of the new compounds were determined on the basis of 1D‐ and 2D‐NMR spectroscopy, as well as by high‐resolution mass spectrometry. The new compounds 2 and 3 showed potent cytotoxic activities against A‐549 and HCT‐116 cell lines.