The structural attributes of the planktonic community, such as abundance, size-structure or taxonomic diversity, are emergent properties of processes taking place at the cellular, individual level. The analysis of individual cells could be applied to the study of the ecosystem dynamics, both in structural and physiological terms. Techniques for the analysis of individual cells of the planktonic community have emerged in the last decades. The Flow Cytometer and Microscope (FlowCAM) is an automatic sampling device that allows the acquisition of information on a single cell basis. In the last years, standardized methodology for the use of FlowCAM has developed which allows to estimate abundance, biomass and size structure of phytoplankton community with reliability, compared to traditional techniques for plankton enumeration. Coupled with automatic classification of images, this methodology allows the identification of phytoplankton cells in broad groups, such as diatoms, dinoflagellates, ciliates and silicoflagellates. Recently, FlowCAM has been oriented to the estimation of intracellular content of different macromolecules, such as pigments or lipids. We explored the relationship between the emission of fluorescence of phytoplankton single cells measured by the FlowCAM and their chlorophyll content. Hence, from a routine analysis of natural samples it is possible to estimate quantitatively the chlorophyll content of single cells, which relates with the photosynthetic rates of the phytoplankton community and could help in the description of photoacclimation processes.