Monitoring and understanding the impact of environmental changes on biodiversity is an important scientific issue for decades. The study of phytoplankton biodiversity in the marine environment is from particular interest, because microalgae largely contribute to the marine biodiversity and represent the basis of the foodweb. Cryptophytes are a most common group in the phytoplankton. In general, the study of biodiversity is heavily dependent on reliable species identification. In this respect, Cryptophytes are very challenging, because they lack distinct discriminating morphological features. Very often, they vary in cell shape or colour within a species. Therefore, classical identification of Cryptophytes is based on ultrastructural features and electron microscopy. The EU-project MICROPAD aimed at facilitating the study of Cryptophyte biodiversity by the application of molecular methods. A set of specific molecular probes has been developed for the identification of Chryptophyta based on differences in the 18S rDNA-sequence. The probes were used in combination with DNA-microarrays and FISH. We report about experiences and data that were generated while accomplishing the aims of the EU-project MICROPAD.