In the present study, fibrinolytic compounds were screened from marine microorganisms. Fungi and actinomycetes, Geomyces sp., Penicillium sp., and Aureobasidium pullulans, etc, were evaluated for their effects on plasminogen using a natural marine fibrinolytic compound FGFC1 as a positive control. It is the first report that Geomyces pannorum has the fibrinolytic activity in vitro. Six compounds of metabolites from Geomyces pannorum, tridec-1-ene (1), methyl (5Z,9Z)-octadeca-5,9-dienoate (2), (E)-icos-4-ene (3), hexyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl) propanoate (4), 5α,8α-epidioxy ergosta-6,22-diene-3β-ol (5) and dibutyl phthalate (6), were isolated and their structures were elucidated by 1H NMR, 13C NMR, 1H–1HCOSY, HMBC, HMQC and MS spectrum. They were identified as long chain fatty acid, sterol and aromatic hydrocarbon, whose fibrinolytic activities were estimated. The results showed that rediscovering rare compounds 2, 3, 5 and 6 could potentially activate the plasminogen and it also showed moderate fibrinolytic activities in vitro with EC50 values of 120.0, 181.3, 200.0 and 179.7 μg/mL, respectively. Accordingly, the results disclosed that Geomyces sp. might have abundant and cultivable microorganisms with potential metabolites for antithrombotic drugs application in biopharmaceutical industries.