Three new thrombin and trypsin inhibitors, cyclotheonamides C (3), D (4), and E (8) were isolated from the marine sponge Theonella swinhoei. Their structures were determined by spectral and chemical methods. Cyclotheonamides A (1) and B (2) are potent thrombin inhibiting cyclic peptides isolated from the Japanese marine sponge Theonella swinhoei. They contain two unusual amino acids, α-ketoarginine (K-Arg) and vinylogous tyrosine (V-Tyr), which are involved in binding to the thrombin molecule. Cyclotheonamides are also strong inhibitors of other serine proteases. Further investigation of the extract of T. swinhoei which had a bright yellow interior led to the isolation of cyclotheonamides C (3) and D (4) along with three artifacts (5-7), while a morphologically-different T. swinhoei afforded cyclotheonamide E (8). This paper deals with the isolation, structure elucidation, and enzyme inhibitory activity of these compounds.