Abstract: Little is known about microbial processes and the effect that viruses have on Synechococcus spp. in aquatic environments. This study investigated diel variations in the Synechococcus spp. abundance in three size-fractionated water samples (200, 10, and 2 μm fractions). Experiments diluting Synechococcus spp. with virus-free water (30 kDa filtrate) in winter months were performed. We found Synechococcus spp. to be more abundant in virus-diluted water than in the other fractions during night time. These results suggest that protozoan grazing did not contribute importantly to a reduction in Synechococcus spp. abundance but that viral lysis more likely caused Synechococcus spp. mortality in these marine coastal waters during winter.