Mesoscale features are recurrently found in the Coastal Transition Zone (CTZ) off central-southern Chile (~35-40°S), a region characterized by seasonal wind-driven coastal upwelling. In this study, oceanographic data from two consecutive cruises carried out during the upwelling season (January 2009) were combined with satellite time series data in order to characterize the structure and evolution of mesoscale eddies and to explore their influence on phytoplankton structure and nutrient distribution, in the context of organic carbon exchanges between the coastal upwelling zone and the CTZ. Two coastally-generated, contiguous mesoscale eddies (~2months old) were characterized: a surface cyclonic eddy (CC1) and a subsurface anticyclonic eddy (AA1). The distributions of salinity and dissolved oxygen, together with nutrients, suggested that both eddies were sites of vertical injection of high nutrient concentrations from the Equatorial Subsurface Water mass (ESSW) into the upper layer in the CTZ. In addition, eddy AA1, in combination with an upwelling plume, was involved in the offshore advection of nutrients from the core of the ESSW located in the coastal zone. At shallow depths (<50m), both eddies displayed moderate chlorophyll-a concentrations (up to 1mgm-3 in CC1 and 3mgm-3 in AA1) compared with the coastal maximum values (up to 18mgm-3). The photosynthetic communities within the eddies were mostly dominated by small cells (picoplankton in CC1 and nanoplankton in AA1) in contrast to microplankton dominance in the coastal band. These results support the view that relatively young mesoscale eddies, both the surface cyclonic and subsurface anticyclonic types, which originate in the coastal band of EBC regions, are important as sites of elevated nutrient concentrations which, in turn, can promote enhanced chlorophyll-a levels in the CTZ.