Cyanobacteria produce oligopeptides that are predominantly synthesized by the non-ribosomal pathway. Among these are the aeruginosin and cyanopeptolin protease inhibitors, which act against enzymes known to cause several human health problems. Atomic force microscopy (AFM) was used to study the effect of cyanopeptides produced by Microcystis aeruginosa NPCD-1 on pathogenic bac-terial cell surfaces. The selected strain was characterized based on the 16S rRNA gene sequence and the intergenic spacer region of the phycocyanin operon. PCR amplification was employed to investigate the presence of genes encoding for aeruginosin and cyanopeptolin. Purified extract from M. aeruginosa NPCD-1 cells was screened for bioactive compounds. The effect of purified extract containing pro-tease inhibitors produced by the NPCD-1 strain on bacterial cells was observed using AFM. Aeruginosin and cyanopeptolin genes were confirmed by both PCR amplification and gene sequencing. Mass spectrometry analysis confirmed the production of aeruginosin. The in-teraction of Bacillus cereus, Escherichia coli and Staphylococcus aureus with cyanopeptides was characterized by examining the loss of surface stiffness and the formation of micelles, most likely originating from the membrane disruption. The AFM results demonstrate the ability of cyanobacterial extract to alter the cellular membrane of bacterial pathogens.