The Patagonian Sea in Argentina is known as an area with high primary production and biodiversity. The complex hydrodynamic environment resulting from the interaction between the Malvinas–Brazil convergence and the waters over the continental shelf and slope enhances the development of high chlorophyll concentrations, especially in frontal and coastal areas. The composition, distribution and variability of several phytoplankton functional types (PFTs) derived from diagnostic pigments were studied in relation to the local hydrographical conditions, using data from a research cruise carried out on board the RV Bio Hesperides at the end of the Summer season (March 2008).Phytoplankton cell size and PFT distributions were found to be highly influenced by the physical and chemical characteristics of the studied environments. Thus large cells, mainly diatoms, were the dominant size fraction in the southern frontal areas, where the SubAntarctic Surface Waters (SASW) from the Malvinas Current meet shelf waters. However, other groups of microphytoplankton (mPF), mainly dinoflagellates, were also detected in the shallow waters zone influenced by the tidal regime near the Valdes Peninsula. Picophytoplankton (pPF) was an important contributor to the floristic composition in the southern frontal zones, while nanophytoplankton (nPF) was dominant in the stations located over the continental slope, and in the oligotrophic area near Mar del Plata.The ratio between photoprotective and photosynthetic pigments (PPC:PSC) and the photoprotection index (PI) indirectly provide information about the environment and its effect on the PFTs composition.