Direct inhibition of blood coagulation factors such as thrombin, factor VIIa, and factor Xa has shown great promise for treating thrombosis disorders. Inhibitors of these serine proteases have been designed, synthesized, and evaluated. Small molecule thrombin inhibitors typically contain P(1)-P(2)-P(3) components targeting the active binding site. Structure optimizations on the P(1) position and the P(3) position have been done extensively, but the P(2) position has not been as thoroughly studied as the other positions. Thrombin inhibitors with a rigid bicyclic P(2) unit are interesting compounds with a more defined conformation. Aeruginosins are a family of naturally occurring small molecules that exhibit serine protease inhibition activities; their structures are typically tetrapeptides with an unusual bicyclic amino acid core structure occupying the P(2) position. About 21 compounds sharing the same core structure have been isolated and identified so far, and their analogs have also been synthesized. In this review, the Structure Activity Relationship (SAR) of these compounds against thrombin and other serine proteases and their potential as antithrombotic agents will be discussed. The binding modes to thrombin and other factors of the coagulation cascade and the preparation of the aeruginosin core structure will be summarized. Besides the aeruginosin family, the SAR of other small molecule serine protease inhibitors with a rigid bicyclic P(2) unit will also be covered.