Abstract: To obtain compounds with allelopathy on bloom microalgae, 28 strains of marine macroalgae-endophytic fungi were tested, and four strains in which crude extracts of the secondary metabolites showed apparent allelopathy on Anabaena flos-aquae and Microcystis aeruginosa were obtained. The four strains were cultured in 15 L of PDB culture and the algicidal activities of 32 compounds isolated from the secondary metabolites were examined. The inhibition ratios of sterigmatocystin, (2'E,4'E,6'E)-6-(1'-carboxyocta-2',4',6'-triene)-11,12-epoxy-9,11-dihydroxydrim-7-ene, 6,8-di-O-methylnidurufin and aversin on A. flos-aquae were all significantly higher than 50% (P < 0.05), and the EC_50,24h values were 6.865 μg/mL, 4.302 μg/mL, 1.824 μg/mL and 2.319 μg/mL, respectively. The inhibition ratios of sterigmatocystin,(2'E,4'E,6'E)-6-(1'-carboxyocta-2',4',6'-triene)-11,12-epoxy-9,11-dihydroxydrim-7-ene and indol-3-carboxaldehyde on M. aeruginosa were all significantly higher than 50% (P < 0.05), and the EC_50,24h values were 4.167 μg/mL, 8.386 μg/mL and 5.374 μg/mL, respectively.