Six secondary metabolites including a new aminobenzoic peptide seco-clavatustide B (1) and a new clavatoic acid derivative 5-acetyl-2,4-dihydroxy-3-methylbenzoic acid (3), were characterized from the EtOAc extracts of the Ascidian-derived endophytic fungus Aspergillus clavatus AS-107. The absolute configuration of compound 1was established by electronic circular dichroism quantum calculation and the structure of compound 3 waselucidated on the basis of spectroscopic data together with single-crystal X-ray diffraction experiment. Theisolated compounds were tested for antimicrobial activities against human and aquatic pathogenic bacteria.Compounds 1 and 2 showed potent activity against aquatic pathogens Aeromonas hydrophilia and Pseudomonas aeruginosa with MIC values of 8.2 and 8.8 μM, respectively.