Synechococcus is a cosmopolitan genus of picocyanobacteria living in the photic zone of freshwater and marine ecosystems. Here, we describe the isolation of 46 closely related picocyanobacterial strains from the Baltic Sea. The isolates showed considerable variation in their cell size and pigmentation phenotypes, yielding a colorful variety of red, pink and blue-green strains. These pigmentation phenotypes could not be differentiated on the basis of their 16S rRNA-internal transcribed spacer (ITS) sequences. Thirty-nine strains, designated BSea, possessed 16S rRNA-ITS sequences almost identical with Synechococcus strain WH5701. Despite their similar 16S rRNA-ITS sequences, the BSea strains separated into several different clusters when comparing the phycocyanin (cpcBA) operon. This separation was largely consistent with the phycobiliprotein composition of the different BSea strains. The majority of phycocyanin (PC)-rich Bsea strains clustered with WH5701. Remarkably, the phycoerythrin (PE)-rich strains of BSea formed an as yet unidentified cluster within the cpcBA phylogeny, distantly related to other PE-rich groups. Detailed analysis of the cpcBA operon using neighbour-net analysis indicated that the PE-rich BSea strains are probably endemic for the Baltic Sea. Comparison of the phylogenies obtained by the 16S rRNA-ITS, the cpcBA, and the concatenated 16S rRNA-ITS and cpcBA operon sequences revealed possible events of horizontal gene transfer among different Synechococcus lineages. Our results show that microdiversity is important in Synechococcus populations and that it can reflect extensive diversification of different pigmentation phenotypes into different ecological niches.