Picocyanobacteria of the genus Synechococcus are a widespread component of marine planktonic communities and are seasonally dominant in the Baltic Sea. It has been shown that light, salinity, temperature, nutrients and grazing influence the niche segregation of Synechococcus. It is known that many Synechococcus strains have allelopathic properties, but the role of allelopathy remains unknown. Recent studies in two-species systems have provided experimental evidence for increased diversity at intermediate levels of allelopathy, while extreme levels (low or high) led to reduced diversity. Here we studied the role of Synechococcus allelopathy in structuring coexisting phytoplankton communities. We brought natural phytoplankton communities from the Baltic Sea to equilibrium in semi-continuous cultures under nitrate limitation. These communities were inoculated with two Synechococcus strains from the Baltic Sea (BA-124; BA-132) known to have allelopathic properties, with different inoculum sizes: low, medium and high, as a proxy of the strength of allelopathy. According to classical resource competition theory, the dominant species at equilibrium (and therefore community diversity) should be the same irrespective of the initial inoculum of any species. Our equilibrium communities were dominated by 2-4 genera, with diatoms predominating at all Synechococcus inoculum levels. Community diversity was significantly higher only at the medium size of Synechococcus inoculum, with strain BA-124. This was the expected effect of allelopathy, according to previous works in two-species systems. There is no other known factor that could produce such an effect considering our experimental design. Therefore, we state that allelopathy is the best hypothesis to explain these results. In strain BA-132, the allelopathic effect appeared to be weaker and had no effect on community diversity. These results are the first to show the influence of allelopathy on the structure of relatively complex phytoplankton communities, suggesting a new driving factor of phytoplankton succession in the Baltic Sea.