A new sesquiterpene, (+)-S-1-methyl-abscisic-6-acid (1), together with five known compounds, (+)-S-abscisic acid (2), fusicoccin J (3), 3α-hydroxyfusicoccin J (4), (R)-5-hydroxymethylmellein (5) and 4-hydroxyphenethyl acetate (6) was isolated from the fermentation extract of Phomopsis amygdali, an entomogenous fungus isolated from Call midge. Their structures were determined mainly by analysis of MS and NMR spectroscopic data. Compounds 1-6 were tested for antimicrobial activity against three plant pathogenic fungi: Gibberella zeae, Verticillium albo-atrum, and Fusarium nivale, and two bacteria: Escherichia coli and Pseudomonas aeruginosa 2033E. As a result, compounds 1-4 displayed antibacterial activity against Gram-negative P. aeruginosa 2033E, and the minimum inhibition concentration (MIC value) of 1-4 is 30 μg/mL, 58 μg/mL, 26 μg/mL, and 26 μg/mL, respectively.