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Two coastal zones (influenced by the Coatzacoalcos and Grijalva-Usumacinta rivers) and an oceanic one (Campeche Canyon), from the southern Gulf of Mexico, were sampled during the ‘nortes’ or windy (February, 2004) season, to study the concentration and distribution of the phytoplanktonic pigments and the picoeukaryote fraction. Vertical profiles of accessory pigments indicated the presence and potential importance of autotrophic picoplankton in the waters of the Southern Gulf of Mexico. These pigments showed different distributions, associated with different hydrographic conditions between the oceanic zone and the coastal regions (e.g. presence and depth of a thermocline), indicating contrasting phytoplankton communities. The highest concentrations of accessory pigments (fucoxanthin, zeaxanthin, divinyl-chlorophyll a) were associated with shallow coastal zones (above 1% PARI), except for prasinoxanthin that also showed high concentrations in the Campeche Canyon. Pigments associated with prokaryotic picoplankton (zeaxanthin, divinyl-chlorophyll a) were more distinguishable in the Campeche Canyon than in the coastal zones. Chlorophyll a was not directly related to accessory pigments in most of the stations studied. Relatively high cell abundances of Prasinophyte Micromonas pusilla occurred at one coastal zone station, using molecular probes (FISH-TSA), and revealed the potential importance of this Prasinophyte in the picoeukaryote fraction from the study area, providing a new insight into their ecological role, relative to diatoms and coccolithophorids. [ABSTRACT FROM AUTHOR]