The Northern Humboldt Current Ecosystem, located along the Southeastern Pacific off Peru, is considered as one of the most productive natural system in the world, being of great relevance the study of phytoplankton as the basis of the marine trophic web. Based on the relationships between the cell surface, biovolume and maximum linear dimension of the cells of the phytoplankton species, 140 species were found in the functional group 'R' (ruderal species, adaptable to high mixing conditions); 133 species in functional group 'S' (stress-tolerant species, predominant in oligotrophic and high light conditions) and 19 species in functional group 'C' (competitive, opportunistic species, predominant in mesotrophic and high light conditions). These three groups are respectively composed of elongated, pennate, and chain-forming diatoms (group R); dinoflagellates, large central diatoms and silicoflagellates (group S) and coccolithophores, some mixotrophic dinoflagellates and phytoflagellates (group C). Coincidence percentages between the functional groups classification of the present study and the ecological classification were between 52% and 90 %. The use of functional groups is proposed to evaluate the spatio-temporal variations of phytoplankton and its relation with environmental conditions in the Northern Humboldt Current Ecosystem.