As a part of our continuing work to discover bioactive leading molecules from marine microorganism, ethyl acetate fraction of organic extract of the train Stachybotrys longispora FG216 showed fibrinolytic activity in our primary screen. The bioassay-guided purification of the active fractions resulted in isolation of a new isoindolone, FGFC2 (1) (FGFC2, Fungi fibrinolytic compound 2), together with two known compounds, LL-Z1272β (2) and ergosterol (3). The structure of compound 1 was elucidated by the spectral analysis of 1D ( 1 H, 13 C) NMR, 2D (COSY, HSQC, and HMBC) and ESI-MS. Three compounds were evaluated for fibrinolytic activities in vitro. Compared to FGFC1 (EC 50 =47 μmol/L) as a reference drug, compound 1 and ergosterol (3) showed moderate fibrinolytic activities in vitro with EC 50 values of 108.16 and 156.30 μmol/L, respectively. LL-Z1272β (2) had no fibrinolytic activity.