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