Flow cytometry is a valuable tool for the analysis of phytoplankton and other suspended particles because of its speed and quantitative measurements, but the method's oceanographic application has been limited by the need to take discrete water samples for analysis on board ship or in the laboratory. For this reason, we have developed an automated flow cytometer (FlowCytobot) that can operate in situ and unattended. The new instrument utilizes a diode-pumped 532nm laser and can measure light scattering and fluorescence of particles as small as Synechococcus cells. For operation at the LEO-15 mooring site off New Jersey, it is connected to shore by power and communications cables, and is controlled by a microcomputer whose programming can be loaded remotely. The sampling rate is adjustable; we have used from 12.5 to 50μlmin−1. Integrated signals from each particle (two light scattering angles and two fluorescence emission bands) are transmitted to a shore-based computer, where they are accessible by Internet and can be examined in real time. FlowCytobot was deployed at LEO-15 from late July to early October 2001, where it operated continuously (aside from occasional power or communications interruptions at the node) without outside intervention. Even after 2 months of in situ operation, FlowCytobot's measurements were similar to those of a conventional flow cytometer, as shown by analysis of a discrete water sample taken at the location of the sample inlet. In addition to documenting seasonal and event-scale changes in size distributions and population abundances in the pico- and nanophytoplankton, FlowCytobot will be useful for examining diel cycles in light scattering and pigment fluorescence of cells in situ that may allow estimation of rates of production by different phytoplankton groups.