Synechococcusis a cosmopolitan marine cyanobacterial genus, and is often the most abundant picocyanobacterial genus in coastal waters. Little is known aboutSynechococcusseasonal dynamics in coastal zones highly impacted by upwelling. This was investigated by collecting seasonal samples from an upwelling-impacted Monterey Bay (MB) monitoring station M0, in parallel with measurements of oceanographic conditions during 2006–2008.Synechococcusabundances were determined using quantitative PCR (qPCR) assays and flow cytometry (FCM). A new qPCR assay was designed to target dominantSynechococcusin MB using therbcLgene, while previously designed assays targeted distinct phylotypes (callednarBsubgroups) with thenarBgene. TherbcLqPCR assay successfully tracked abundantSynechococcusin MB, accounting for on average 89% (± 57%) of FCM-based counts. Annual spring upwelling caused decreases inSynechococcusandnarBsubgroup abundances. Differences innarBsubgroup abundance maxima and abundance patterns support the view that subgroups differ in their ecologies, including subgroup D_C1, which seems to specifically thrive in coastal waters. Correlations betweennarBsubgroup abundances and measured environmental variables were similar among the subgroups. Therefore, non-measured environmental factors (e.g. metals, mortality) likely had different influences on subgroups, which led to their distinct abundance patterns at M0.