A fast and reliable identification of nano- and picoplankton by light microscopy is often difficult because of the lack of usable morphological characteristics, whereas electron microscopy and biochemical methods, such as HPLC, are very time consuming. One possibility to solve this problem is to use taxon specific rRNA probes. For this purpose we searched an algal ribosomal rRNA sequence database for small unique regions to be used as probes to differentiate phytoplankton taxa. These probes were either labelled with Digoxigenin (DIG) and used in DNA dot blot experiments, or labelled with fluorochromes and used in whole-cell hybridisations with fluorescence microscopy or flow cytometric detection. Specific probes could be used over a broad taxonomic range from higher groups (i.e. dinoflagellates) to species level (i.e., Prorocentrum micans). These probes will be used in the EU MAST project AIMS for the development of an automated identification system for marine phytoplankton in combination with flow cytometry and artificial neural networks (ANN)and in the German national project (TEPS) for the development of an early warning system for harmful algal blooms. Illustrations are provided to highlight specific problems with dinoflagellate whole-cell hybridisations. This work was supported by the German BMBF TEPS 03F0161 and the EU AIMS MAS3-CT97-0080 projects.