An isoindolone derivative, Fungi fibrinolytic compound (R)‐2,5‐bis((2R,3R)‐2‐((E)‐4,8‐dimethylnona‐3,7‐dien‐1‐yl)‐3,5‐dihydroxy‐2‐methyl‐7‐oxo‐3,4,7,9‐tetrahydropyrano[2,3‐e]isoindol‐8(2H)‐yl)pentanoic acid (FGFC1, Fungi fibrinolytic compound 1), was isolated from a rare marine microorganism strain Stachybotrys longispora FG216. The structure of FGFC1 was elucidated by 1H NMR, 13C NMR, IR, and MS data; moreover, it was also evaluated for fibrinolytic activity in vitro and in vivo. The results showed that 0.1–0.4 mmol/L of FGFC1 could stimulate generation of plasmin activity (increased by 2.05–11.44 folds) by measuring Glu‐plasminogen and Lys‐plasminogen activation in vitro. The experiment of fluorescein isothiocyanate (FITC)‐fibrinogen degradation indicated that the effect of FGFC1 on fibrinolytic activity was mediated by plasminogen and scuPA. In addition, FGFC1 (10 mg/kg) could dissolve most of pulmonary thrombus of Wistar rat in vivo. It is possible that FGFC1 is a potential thrombolytic agent in the future.