Fluorescently-labelled molecular probes can identify and characterise phytoplankton species by in situ hybridisation with adjacent detection by fluorescence microscopy or flow cytometry. More or less conserved regions on the rRNA genes make it possible to develop probes that are specific for different taxonomic levels from higer groups, like eukaryotes, down to species and even strain level. These hierarchical probes can be used to estimate biodiversity at a variety of taxonomic levels and are a valuable tool for analysing microalgae and answering ecological questions.