We are exploring the development and application of large-subunit rRNA (LSU rRNA)-targeted oligonucleotide probes as tools to aid in the detection and enumeration of the fragile, fish-killing raphidophytes. Oligonucleotide probes potentially specific for Heterosigma akashiwo and Fibrocapsa japonica, as well as raphidophytes in general, were evaluated using whole cell fluorescent in situ hybridization (FISH). Probes that reacted strongly towards the target organisms and displayed promising specificity were then incorporated into a sandwich hybridization assay (SHA), and evaluated on the basis of their ability to detect and quantify the target organisms in cultured and natural samples. Species-specific SHA‚s were successfully developed for both H. akashiwo and F. japonica, and the sensitivity of these tests is such that resource managers could utilise the assay to detect these species at concentrations well below those that result in fish mortality. Batch culture experiments showed that the response of the SHA towards a constant number of H. akashiwo and F. japonica cells harvested in exponential versus stationary phase of growth varied by a factor of approximately two, except for dying cells of H. akashiwo in late stationary phase. Using the FISH method, cells reacted poorly towards the probes after entering the late stationary phase of growth. The difference between results of the FISH and SHA-based tests suggests that the rRNA in preserved, intact cells is less accessible to the probes than is rRNA released upon cell lysis. The SHA, applied using an automated robotic processor, appears to be a faster, more cost-effective, and easier-to-use method than other cell detection and quantification strategies for H. akashiwo and F. japonica based on FISH or light microscopy, particularly when large numbers of samples must be processed routinely and rapidly.