The marine cyanobacterium Synechococcus plays an important role in microbial food webs and is a significant contributor to primary production in the world's oceans. The abundance distribution of picoplanktonic Synechococcus was investigated in the Gulfs of Bandirma and Erdek (in the Sea of Marmara), in which water samples were taken seasonally between August 2007 and August 2008 during an intense period of mucilage formation. The mucilage phenomenon occurred in the Sea of Marmara between October 2007 and February 2008. In both sites, Synechococcus abundance was highest in November 2007, at 32.68 x 10(4) cells ml(-1) in the Gulf of Bandirma and 34.83 x 10(4) cells ml(-1) in the Gulf of Erdek, with the high values in November 2007 coinciding with mucilage formation. In contrast, the lowest Synechococcus abundance was 0.85 x 10(4) cells ml(-1) in February 2008 in the Gulf of Bandirma and 3.27 x 10(4) cells ml(-1) in May 2007 in the Gulf of Erdek. The two-layered structure of the Sea of Marmara affected the vertical distribution of Synechococcus, in which the maximum abundance of Synechococcus occurred in the upper layers and the minimum abundance values at the deeper layers of both gulfs. This layered structure also strongly affected the relationship between Synechococcus and environmental parameters. In this sense, Synechococcus abundance was negatively correlated with salinity and nitrate but was positively correlated with chlorophyll-a in the Gulfs of Bandsrma and Erdek but was not correlated with temperature or phosphate in either gulf. Despite the fact that Synechococcus is temperature dependent, the abundance distribution was influenced more by other environmental factors than by temperature.