From 2000 to 2016, substantial changes in biomass and community structure of small pelagic fish and mesozooplankton have been reported in the Bay of Biscay. Since significant relationships have been found between phytoplankton chlorophyll a and mesozooplankton as well as between phytoplankton chlorophyll a and shifts in sardine body condition, it was hypothesized that phytoplankton communities may have also been affected during this period and may have played a role in these changes. However, the available data were insufficient to validate this hypothesis and the causes of these changes remained unexplained. The present study analyzed a spatio-temporal marine microphytoplankton dataset collected during the annual PELGAS (PELagiques GAScogne) surveys from 2003 to 2014. The thorough analysis of microphytoplankton taxonomic composition, with an approach integrating the relative role of environmental conditions as well as biotic interactions and applying the concept of ecological niche, confirmed that significant modifications in microphytoplankton community structure occurred during this period. Temporal changes were stronger than spatial differences at these sampling scales. Three main periods, 2003-2005, 2006 and 2007-2014, showing different community structure, diversity and dominant taxonomic units were highlighted. Twenty eight taxonomic units were involved in these community changes. Among them, five were identified as the protagonists (Pseudo-nitzschia spp., Gymnodinium spp. + Gyrodinium spp., Leptocylindrus danicus, Leptocylindrus minimus and Chaetoceros sp.). Variations in water temperature and equivalent freshwater depth constrained the realized ecological niches of these species and explained, at least in part, changes in community structure. This study stresses the need to improve our knowledge of phytoplankton species ecological niches and to take into account biotic interactions for a thorough understanding of the processes shaping plankton communities and the resulting diversity patterns.