The division Cryptophyta, Class Cryptophyceae, contains ecologically important species that are found in all kinds of aquatic habitats. The identification of the Cryptophyta is challenged by a need to examine species in the SEM or TEM to visualize features needed to identify its species. Thus, for routine monitoring programmes, this group is not identified beyond the level of class and that identification is only done if the samples are routinely examined with a fluorescent microscope and the cryptophytes are counted based on the natural orange fluorescent of their phycobilin pigments. We present a set of molecular probes that target the 18S rDNA of the class Cryptophyceae and its major clades. This includes two probes at the level of class and 12 probes to distinguish the different clades, which should be amended to the level of family or genus. Within the Cryptophyceae, seven clades have been described previously, which do not correspond to the present day classification of the group. The probes can be used for a multiplexed analysis on a PHYLOCHIP, which allows a rapid characterization of Cryptophyceae in field samples. The probes have been tested for specificity and their applicability on a DNA-microarray proven. © The Author 2007. Published by Oxford University Press. All rights reserved.