The Mozambique Channel is a region of high marine biodiversity. Thes resources provide assistance to coastal communities in the riparian countries, having important industrial and artisanal fisheries. Futhermore, this region is caracterised by a strong meso-scale activity (cyclonic and anticyclonic eddies) that have a important impact on the primary production. The main goal of this PhD thesis is to understand and to improve our predictive capabilities of the influence of the meso-scale oceanography on the development and structuring of ecosystems in the Mozambique Channel. To achieve this goal, we will develop an integrated model of the Mozambique Channel ecosystem hydrodynamics – biogeochemistry - ecology. We will couple an oceanographic model (ROMS), a biogeochemistry model (PISCES) and an ecosystem model (APECOSM) to analyse the biophysical processes responsible for the meso-scale structuring of the pelagic ecosystem in the Mozambique Channel.