Fractionation of the ethyl acetate extract of the marine bacterium Bacillus pumilus isolated from the black coral Antipathes sp. led to the isolation of five compounds: cyclo-(L-Leu-L-Pro) (1), 3-hydroxyacetylindole (2), N-acetyl-β-oxotryptamine (3), cyclo-(L-Phe-L-Pro) (4), and 3-formylindole (5). The structures of compounds 1-5 were established by spectroscopic analyses, including HRESITOF-MS and NMR (1H, 13C, HSQC, HMBC and COSY). Compounds 2, 3 and 5 caused the inhibition on the growth of Trypanosoma cruzi (T. cruzi), with IC50 values of 20.6, 19.4 and 26.9 μM, respectively, with moderate cytotoxicity against Vero cells. Compounds 1-5 were found to be inactive when tested against Plasmodium falciparum and Leishmania donovani, therefore showing selectivity against T. cruzi parasites.