ABSTRACT. – The division Cryptophyta, Class Cryptophyceae, contains ecologically important microalgae that are found in all aquatic habitats. The identification of the Cryptophyta is challenged by a need to examine species in the scanning electron microscope or transmission electron microscope (SEM or TEM) to visualise features needed to identify species. Thus, for routine monitoring programs, this group is not usually identified beyond the level of class and that is done only if the samples are routinely examined by the optic Utermöhl method. Here we present an analysis of field samples taken from Arcachon Bay taken in summer 2006 and analysed with probes made for different clades within the Cryptophyta and counted with a solid phase cytometer, the ChemScan. Our results show that the molecular counts were lower than cell counts made by optic method and this is likely because of cell loss from delay in processing the samples and cell rupture from fixation. Nevertheless, clade 3, composed of the genera Rhinomonas, Rhodomonas, Pyrenomonas and Storeatula, were the most numerous in Arcachon Bay in 2006.