A mixed community composed of a non-toxic form of Alexandrium tamarense and a paralytic shellfish poisoning (PSP) toxin-producing A. minutum develops on an annual basis in Cork Harbour, Ireland. The understanding of the ecological mechanisms that influence the population dynamics of these bloom-forming species is fragmentary, partly due to the difficulty in the discrimination between Alexandrium species in mixed phytoplankton assemblages by conventional light microscopy. During 2 surveys carried out in the estuary in July and September 2005, taxon-specific large subunit rRNA targeted probes were used in a whole-cell fluorescent in situ hybridisation assay to facilitate the detection and quantification of Alexandrium spp. in seawater samples. The Alexandrium spp. concentrations derived with molecular probes were on average half those obtained using an Utermohl sedimentation chamber and calcofluor. Results showed the dominance of A. tamarense over A. minutum in July and an almost exclusive presence of A. minutum in September. Alexandrium spp. did not quantitatively dominate the total dinoflagellate assemblage and cell concentrations were lower than those found in bloom situations, nonetheless reaching more than 1 x 10(4) cells l(-1) locally on both occasions. The PSP toxins GTX3 and GTX2 were detected in all field samples, concentrations being associated with greater abundances of A. minutum in September. Despite probable inaccuracies inherent in the sampling methodology, the estimated intracellular toxin quotas in A. minutum were higher in the areas of the estuary that connected different water bodies and where cells may be subjected to regimes of high turbulence and rapid changes of salinity and temperature.