We collected samples monthly, from April to August 1998, to measure the abundance of autotrophic picoplankton in San Francisco Bay. Samples taken along a 160-km transect showed that picocyanobacteria (Synechococcus sp.) was a persistent component of the San Francisco Bay phytoplankton in all the estuarine habitats, from freshwater to seawater and during all months of the spring–summer transition. Abundance ranged from 4.6 ± 10⁶ to 5.2 ± 10⁸ cells L^-1, with peak abundance during the spring bloom (April and May) and during July with a persistent spatial pattern of smallest abundance near the coastal ocean and highest abundance in the landward domains of the estuary. The picocyanobacterial component (as estimated percentage of chlorophyll a concentration) was, on average, 15% of total phytoplankton biomass during the summer– autumn nonbloom periods and only 2% of chlorophyll biomass during the spring bloom. This result is consistent with the emerging concept of a gradient of increasing importance of picocyanobacteria along the gradient of decreasing nutrient concentrations from estuaries to the open ocean.