Abstract Phytoplankton populations were analyzed using flow cytometry in monthly samples at the Bermuda Atlantic Time-series Study (BATS) station in the Sargasso Sea from 1989–1994 for picoplankton ( Synechococcus and Prochlorococcus ) and from 1992–1994 for eukaryotic phytoplankton in order to better understand the mechanisms that dictate seasonal and inter-annual patterns in the phytoplankton community. The eukaryotic phytoplankton were dominated by populations of small nanoplankton (mostly 2–4 μm diameter), though populations of coccolithophores and sometimes pennate diatoms also could be distinguished. Flow cytometric measurements of population abundances, individual cell light scattering (which can be related to cell size), and chlorophyll fluorescence were made. Synechococcus and the eukaryotic phytoplankton reached their greatest concentrations during the spring bloom each year when the water column was deeply mixed and nutrients were detectable in surface waters. The maximum cell concentration for Prochlorococcus was in the summer and fall of each year, with a deeper sub-surface maximum than Synechococcus . Picoplankton chlorophyll fluorescence and estimated cell size were greater at depth than near the surface, and were lowest in midsummer for both Synechococcus and Prochlorococcus . In the summer and fall, Prochlorococcus cells were often smallest at mid-depth, even when fluorescence per cell and cell concentration were lower at the surface. For the eukaryotes (including coccolithophores), cell concentrations were high during the spring in both 1992 and 1993, and in fall 1992. At these times, mean cell size and fluorescence were low. Improved size and carbon estimates were made and it was found that the estimated contribution of phytoplankton carbon to total particulate organic carbon, integrated over the upper 200 m, averaged 33% (range 21–43%) with no pronounced seasonal pattern.