Among the serine proteases involved in thrombosis and hemostasis, thrombin plays a key role in blood coagulation; for example, it converts fibrinogen into fibrin and activates the co factor V and VIII by a specific cleavage of certain peptide bonds next to arginine in physiological substrates. It also acts as a potent agonist for platelet aggregation. Therefore, thrombin is an effective target for an anticoagulant agent. During our screening program for thrombin inhibitors, we isolated a novel inhibitor, Ro 09-1679 (1), from the culture broth of strain NR6773 collected at Minamishitara, Aichi Prefecture, Japan. The strain was identified as Mortierella alpina Peyronel on the basis of its morphological properties. In this paper, the fermentation, isolation, structural elucidation and biological properties of 1 are reported.