Mesopelagic communities are characterized by a large biomass of diverse macrozooplankton and micronekton (MM) performing diel vertical migration (DVM) connecting the surface to the deeper ocean and contributing to biogeochemical fluxes. In the Southern Ocean, a prominent High Nutrient Low Chlorophyll (HNLC) and low carbon export region, the contribution of MM to the vertical carbon flux of the biological pump remains largely unknown. Furthermore, few studies have investigated MM communities and vertical flux in naturally iron fertilized areas associated with shallow bathymetry. In this study, we assessed the MM community diversity, abundance and biomass in the Kerguelen Island region, including two stations in the HNLC region upstream of the islands, and two stations in naturally iron fertilized areas, one on the Plateau, and one downstream of the Plateau. The MM community was examined using a combination of trawl sampling and acoustic measurements at 18 and 38 kHz from the surface to 800 m. A conspicuous three-layer vertical system was observed in all areas - a shallow scattering layer, SSL, between 10 and 200 m; mid-depth scattering layer, MSL, between 200 and 500 m; deep scattering layer, DSL, between 500 and 800 m - but communities differing among stations. While salps (Salpa thompsoni) dominated the biomass at the productive Kerguelen Plateau and the downstream station, they were scarce in the HNLC upstream area. In addition, crustaceans (mainly Euphausia vallentini and Themisto gaudichaudii) were particularly abundant over the Plateau, representing a large, although varying, carbon stock in the 0–500 m water layer. Mesopelagic fish were prominent below 400 m where they formed permanent or migrant layers accounting for the main source of carbon biomass. Through these spatial and temporal sources of variability, complex patterns of the MM vertical distribution and associated carbon content were identified. The total carbon flux mediated by migratory myctophids at the four stations was quantified. While this flux was likely underestimated, this study identified the main components and mechanisms of active carbon export in the region and how they are modulated by complex topography and land mass effects.