Toxicon, 2013; 70: 21-31Microcystins are cyclic heptapeptides from cyanobacteria which are responsible for poisonings of livestock and humans. Cyanobacteria also produce a range of peptides and other compounds that can result in complex chromatograms when samples are analysed by LC– MS. Thiol derivatization of the a,b-unsaturated amide present in most microcystins was recently shown to simplify analysis of LC–MS chromatograms of a Microcystis culture, making it easier to identify peaks corresponding to microcystins in complex mixtures. This method was applied to analysis of extracts taken from a natural cyanobacteria bloom in Mwanza Gulf, Lake Victoria, Tanzania, in 2010, revealing the presence of numerous putative microcystin analogues in the sample. Results were verified using LC–MS2, LC–MS/MS with precursor-ion scanning, and LC–HRMS, leading to identification of 8 major and 17 minor microcystins in the sample, including analogues of microcystin-RY, -RL and -RA. Microcystin-YR (2), -RR (3), and -RY (9) were isolated from bloom material from Lake Victoria, and the structure of 9 was confirmed by NMR spectroscopic analysis and NMR spectral comparison with 2 and 3. Confirmation of the structure of MC-RY (9) facilitated detailed analysis of its MS2 spectrum, thereby supporting the structures of related analogues tentatively established on the basis of MS analysesThe Norwegian Programme for Development, Research and Higher Education (NUFU PRO 07/10224) and SIDA SAREC: VICRES Endocrine disruptors project (SUA).