A fundamental understanding of the interaction between physical and biological factors that regulate plankton species composition requires, first of all, detailed and sustained observations. Only now is it becoming possible to acquire these types of observations, as we develop and deploy instruments that can continuously monitor individual organisms in the ocean. Our research group at WHOI can measure and count the smallest phytoplankton cells using a submersible flow cytometer (FlowCytobot), in which optical properties of individual suspended cells are recorded as they pass through a focused laser beam. However, FlowCytobot cannot efficiently sample or identify the much larger cells that often dominate the plankton in coastal waters. Because these larger cells often have recognizable morphologies, we have developed a second submersible flow cytometer that provides high-resolution (1 micrometer) images of cells 10 to 100 micrometers in size, in addition to chlorophyll fluorescence and light scattering measurements. Like the original, Imaging FlowCytobot incorporates antifouling strategies that allow it to operate unattended for months at a time; it obtains power from and communicates with a shore laboratory, so we can monitor results and modify sampling procedures when needed. The images are of sufficient quality that cells can be identified to genus or species in many cases; we have developed an automated classification system based on feature extraction and a Support Vector Machine. Imaging FlowCytobot has successfully been deployed for 3 months in Woods Hole Harbor, and we plan to deploy it next alongside FlowCytobot at the Martha's Vineyard Coastal Observatory, 2 km offshore on the northeast United States continental shelf. The combined observations from the two instruments will allow continuous long term observations of plankton community structure over a wide range of cell sizes and types, and help to elucidate the processes and interactions that control the life cycles of individual species.