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Population oscillations in multi-species or even single species systems are well-known but have rarely been detected at the lower trophic levels in marine systems. Nitrogen fixing cyanobacteria are a major component of the Baltic Sea ecosystem and sometimes form huge surface accumulations covering most of the sea surface. By analysing a satellite-derived 39-year (1979-2017) data archive of surface cyanobacteria concentrations we have found evidence of strikingly regular interannual oscillations in cyanobacteria concentrations in the northern Baltic Sea. These oscillations have a period of ~3 years with a high-concentration year generally followed by one or two low-concentration years. Changes in abiotic factors known to influence the growth and survival of cyanobacteria could not provide an explanation for the oscillations. We therefore assume that these oscillations are intrinsic to the marine system, caused by an unknown, probably mainly biological mechanism that may be triggered by a combination of environmental factors. Interactions between different life cycle stages of cyanobacteria as well as between predator-prey or host-parasite are possible candidates for causing the oscillations.