The first KErguelen Ocean and Plateau compared Study (KEOPS1), conducted in the naturally iron-fertilised Kerguelen bloom, demonstrated that fecal material was the main pathway for exporting carbon to the deep ocean during summer (January–February 2005), suggesting a limited role of direct export via phytodetrital aggregates. The KEOPS2 project reinvestigated this issue during the spring bloom initiation (October–November 2011), when zooplankton communities may exert limited grazing pressure, and further explored the link between carbon flux, export efficiency and dominant sinking particles depending upon surface plankton community structure. Sinking particles were collected in polyacrylamide gel-filled and standard free-drifting sediment traps (PPS3/3), deployed at six stations between 100 and 400 m, to examine flux composition, particle origin and their size distributions. Results revealed an important contribution of phytodetrital aggregates (49+/-10 and 45+/-22% of the total number and volume of particles respectively, all stations and depths averaged). This high contribution dropped when converted to carbon content (30+/-16% of total carbon, all stations and depths averaged), with cylindrical fecal pellets then representing the dominant fraction (56+/-19 %). At 100 and 200m depth, iron- and biomass-enriched sites exhibited the highest carbon fluxes (maxima of 180 and 84+/- 27 mgCm-2 d-1, based on gel and PPS3/3 trap collection respectively), especially where large fecal pellets dominated over phytodetrital aggregates. Below these depths, carbon fluxes decreased (48+/-21%decrease on average between 200 and 400 m), and mixed aggregates composed of phytodetritus and fecal matter dominated, suggesting an important role played by physical aggregation in deep carbon export. Export efficiencies determined from gels, PPS3/3 traps and 234Th disequilibria (200m carbon flux/net primary productivity) were negatively correlated to net primary productivity with observed decreases from ~0.2 at low-iron sites to ~0.02 at high-iron sites. Varying phytoplankton communities and grazing pressure appear to explain this negative relationship. Our work emphasises the need to consider detailed plankton communities to accurately identify the controls on carbon export efficiency, which appear to include small spatio-temporal variations in ecosystem structure.