The class Cryptophyceae (Division Cryptophyta) contains ecologically relevant species, which are widespread in aquatic environments. However, classification, identification, and enumeration of cryptophytes are challenged by a morphology that must be usually examined with EM to permit species identification. The quantitative importance of this group has been revealed by HPLC data. But ecological information assessing the occurrence or seasonality of cryptophytes in the marine environment is still scarce. Molecular techniques allow for a refined assessment of taxonomically challenging taxa, such as the cryptophytes. In our laboratory, a Phylochip was developed to facilitate and refine the assessment of cryptophyte microalgae. Here, we present the results of an environmental study that took advantage of the Phylochip. The study was designed to elucidate the seasonality and contribution of cryptophytes to phytoplankton structure in the German Bight. The occurrence of cryptophytes in total plankton versus the picoplankton fraction was assessed with the Phylochip between the years 2004 and 2006. Our data indicate that cryptophytes are an important and constant contributor to phytoplankton structure of the German Bight, especially in the picoplankton fraction.