Dinoflagellates are single-celled protists that make up a significant fraction of phytoplankton, and they are central to both the aquatic food chain and CO2 fixation in Earth's oceans, making them key players in the marine ecosystem. However, the diverse cellular biology of these organisms is undercharacterised. Culturing marine phytoplankton in the lab is challenging, so as part of the Traversing European Coastlines (TREC) Expedition from the European Molecular Biology Laboratory, Paolo Ronchi, Yannick Schwab and colleagues set out to collect samples of plankton from their native environment and analyse their intracellular organisation. In this study (Mocaer et al., 2023), they describe a sampling, preparation and microscopy pipeline that allows them to identify and image plankton in mixed field samples in exquisite detail. Using volumetric correlative light and electron microscopy (vCLEM), the authors quantitatively characterize the 3D ultrastructure of a single cell of the dinoflagellate Ensiculifera tyrrhenica, revealing the subcellular organisation of the chloroplast, mitochondrion, trichocysts and flagella. Furthermore, a detailed picture of the chromosomes, which are permanently condensed in dinoflagellates, suggests that a limited amount of chromatin can be partially unfolded near the nucleolus, allowing for transcription. In the future, combining this method with high-throughput AI image analysis might help to rapidly advance our understanding of phytoplankton cell biology.