The influence of mesoscale physical structures in the phytoplankton taxonomic composition of the subsurface chlorophyll maximum off western Baja California

► Phytoplankton community characteristics were investigated in the SCM off Baja California. ► Taxonomic composition and physiology of phytoplankton was affected by mesoscale eddies. ► High chlorophyll and high physiologic competence were detected in the SCM inside the eddies. ► Outside the eddies the community was dominated by picoplankton groups.