The cyanobacterial strain Microcystis species CAWBG11 was investigated in order to isolate and characterise bioactive oligopeptides such as aeruginosins and microviridins. Liquid Chromatography tandem Mass Spectrometry (LC-MS/MS) Analysis of a methanol extract of a Microcystis CAWBG11 identified four known aeruginosin variants and four putatively new aeruginosin congeners as aeruginosins 618, 656A, 656B and 602B. Planar structures for these new congeners were proposed based on the MS/MS data, in conjunction with the sequence of the known aeruginosins. Amongst the aeruginosins detected there were three pairs, each with the same molecular masses but exhibiting different retention times. Each pair was assigned as stereoisomers since they yielded identical tandem mass fragment ions. The previously reported aeruginosin 602A was further characterised using the Advanced Marfey’s Method of amino acid analysis and Nuclear Magnetic Resonance (NMR) spectroscopy. Four new congeners of the cyclic microviridins; 1778A, 1778B, 1760 and 1764 were detected from a methanol extract of Microcystis CAWBG11. The sample was subsequently purified, enabling a planar structure for each congener to be proposed based on MS/MS data and amino acid analysis. The structure for microviridin 1778A was further investigated by NMR spectroscopy but was not fully elucidated due to time constraints. The presence of the new aeruginosin and microviridin congeners indicated the diversity of the bioactive oligopeptides in the Microcystis strain.