This paper aims at studying numerically the competition between two mutually exclusive phytoplankton species in a fully-turbulent field consisting of interacting mesoscale and submesoscale structures. A simple NPPZD ecosystem model is embedded in a Surface Quasi-Geostrophic model which is able to reproduce frontogenesis and the associated nutrient vertical pump. The two simulated phytoplankton species differ by their size and their affinity for nutrients. In this study, we rationalize the role played by eddies and filaments in the distribution of the two phytoplankton species. We show that the SQG dynamics are responsible for the coexistence of the two phytoplankton species on a single limiting resource at statistical steady state. In addition, we show that as a result of strong vertical injections, filaments contain 64% of the phytoplankton biomass. The two phytoplankton species coexist in filaments but the large phytoplankton is predominant. By contrast, this latter is completely excluded from eddy cores where only the small phytoplankton develops. Since eddies are coherent structures (unlike filaments) and since their edges are almost impermeable to horizontal transport, the large phytoplankton can barely enter eddies. Therefore, eddies are ecological niches which shelter the small phytoplankton. Finally we show that interactions between eddies such as eddy merger can favor the survival of phytoplankton species within eddies on long time scales in the ocean.