The halogenated compounds aeruginosin and cyanopeptolin (protease inhibitors) are well documented in several cyanobacteria. In this work, the presence of genetic coding for aeruginosin and cyanopeptolin in Sphaerocavum genus and their characterization by mass spectrometry and potential toxic effects were investigated. Three strains of Sphaerocavum brasiliense (CCIBt 3094, CCIBt 3096 and CCIBt 3316) isolated from different reservoirs in São Paulo State, and one (CCIBt 3179) from Rio Grande do Norte State were selected for this study. Fragments of aerA-aerB and mcnC-mcnE gene regions (aeruginosin and cyanopeptolin, respectively) were amplified by polymerase chain reaction (PCR) and sequenced. Compounds were characterized by mass spectrometry. All the studied strains presented aeruginosin and cyanopeptolin synthetase genes. Mass spectrometry showed the presence of several aeruginosin and cyanopeptolin variants. The Allium test showed that the ethanolic extract promoted toxic and cytotoxic actions in acute and chronic treatments. These naturally occurring protease inhibitors can play an important role in the physiopathology of human diseases.