There is increasing evidence that bacterial–algal interactions play a role in Harmful Algal Bloom (HAB) ecology. Bacteria that are associated with bloom-forming algal species, specifically toxic dinoflagellate algae, have been implicated in the production and biotransformation of paralytic shellfish toxins (PSTs). To clarify the role that these bacteria may play in the production of PSTs, it is desirable to identify and localize the bacteria associated with the dinoflagellates and enumerate them during the course of the algal blooms that the toxic dinoflagellates produce. Because 16S rRNA-targeted probes offer the possibility of both, we previously made and tested probes for some putatively toxigenic bacteria isolated from cultures of the PSP-related dinoflagellates Alexandrium tamarense, A. affine and A. lusitanicum. The bacteria isolated from the dinoflagellates belong primarily to the alpha-proteobacterial group of Roseobacter and the gamma-proteobacterial group of Alteromonas. Here, we report the successful application of these probes to Lugol's-fixed seawater samples. We detected these bacteria in high numbers in the water column when Alexandrium spp. were both present and absent, and during periods when mussels contained PSTs.