New antibiotics, miyakamides A1, A2, B1, and B2, were isolated from the cultured broth of Aspergillus flavus Link var. columnaris FKI-0739 together with known compounds, parasiticolide A, hydroxyaspergillic acid, and kojic acid. The structure of miyakamide A1 is N-acetyl-L-phenylalanyl-N-methyl-L-phenylalanyl-(alphaZ)-alpha,beta-didehydrotryptamine, and miyakamide A2 is E isomer of A1 at didehydrotryptamine. The structure of miyakamide B1 is N-acetyl-L-tyrosyl-N-methyl-L-phenylalanyl-(alphaZ)-alpha,beta-didehydrotryptamine, and B2 is E isomer of B1. Both miyakamides A1 and B1 existed as equilibrium isomers in solvents, and this isomerism was associated with cis-trans rotation of the amide bond between two amino acids. Conformational isomerism between two amino acids of miyakamides A2 and B2 is cis-form. Miyakamides showed growth inhibitory activity against brine shrimp, Artemia salina.