In order to contribute to the knowledge of potentially toxigenic phytoplankton, the frequency, distribution and abundance of these organisms in samples from eleven cruises conducted in the Colombian Pacific basin from 2004 to 2011 is described. The research cruises were conducted under the Regional Study of the “El Niño” phenomenon in the Southeast Pacific (ERFEN), a multinational program of the Permanent Commission for the South Pacific (CPPS). Genera Pseudo-nitzschia, Dinophysis, Gonyaulax, and Alexandrium are remarkable in the results because of their wide distribution, persistence and abundance. These species have been reported to cause amnesic intoxications (Pseudonitzschia), diarrhea (Dinophysis and Gonyaulax), and paralytic poisoning (Alexandrium). Although some of these species were abundant in the plankton, there were not obvious changes in water coloration or reports of adverse effects during the study period.