Two new diketopiperazine derivatives, bacillusamides A (1) and B (2), have been isolated from the EtOAc extract of the sea urchin-derived Bacillus sp. along with the known cyclo(-L-pro-L-val-) (3), cyclo(-L-pro-L-tyr-) (4), cyclo(-L-pro-L-phe-) (5). These structures were elucidated by extensive spectroscopic methods. Furthermore, the absolute configurations of the amino acid residues were determined using Marfey's method. Compound 1 displayed weak antifungal activity against Aspergillus niger.