Streptomyces species are prolific sources of secondary metabolites, but many biosynthesis gene clusters for secondary metabolite production remain cryptic under standard laboratory conditions. Recent research has illustrated that some mycolic acid-containing bacteria, such as Tsukamurella pulmonis, interact with Streptomyces strains and induce the production of cryptic secondary metabolites by co-culture. In this report, we describe the isolation of arcyriaflavin E (2), a new cytotoxic indolocarbazole alkaloid, along with two known related alkaloids, BE-13793C (1) and arcyriaflavin A (3), from Streptomyces cinnamoneus NBRC 13823 induced by culturing with Tsukamurella pulmonis. The structures of 1 and 3 were determined to be BE-13793C and arcyriaflavin A, respectively, by comparing their molecular formulae, UV spectra and a series of NMR spectra with literature data. The new compound 2 was isolated as an orange powder, its molecular formula was determined to be C20H11N3O3 by HR-Time-of-flight mass spectrometry, and its structure was elucidated via 1D and 2D NMR analyses as the C1-deoxy form of 1 (or the C1-hydroxy form of 3). Cytotoxicity assays against P388 murine leukemia cells showed that 1 and 2 had IC50s of 33 and 39 μM, respectively, while 3 did not show any cytotoxicity up to a concentration of 100 μM. Our results illustrate that the combined culture with mycolic acid-containing bacteria is an efficient and convenient method for searching for novel natural compounds produced by Streptomyces strains.