Measuring biodiversity in the oceans and its modifications with time or during climate change requires the accurate description of plankton organisms from viruses to fishes. However, our taxonomic knowledge of this 70% of the Earth is extremely limited. The ultimate way to perform large-scale taxonomical analysis is to achieve full 3D imaging of every specimen collected. Novel 3D imaging techniques are undoubtedly at the forefront of such efforts, and will provide an important tool to identify, classify and generate reference models (or 3D gold standards) for rapid recognition and classification of plankton organisms during community or basin studies. This review gives an overview of recently developed 3D imaging techniques and discusses their limitations and promises.