Particles located at the interface between the surface ocean layer and the top of the mesopelagic domain are the initial vector of the biological pump yet, their nature is still largely unknown. During the MOBYDICK cruise in the vicinity of the Kerguelen Islands (Indian sector of the Southern Ocean) we deployed a recently available device that concentrates and collects deep particles over a predetermined layer of water. In this paper, we present a detailed description of the collected particles and individual planktonic cells, including their taxonomy, carbon and lipid content, as well as cell viability, in order to characterize the particle stocks present at depth. The cruise was carried out at the end of the summer bloom, a period characterized by declining stocks of biogenic material associated with various mortality processes of planktonic organisms. Unexpectedly, the majority of the collected particles consisted of single empty diatom frustules, while fecal pellets and aggregates accounted for only a minor fraction. Distinct mortality processes, from parasitic infection to mesozooplankton grazing, and distinct silicification degrees as well as different life stages could be identified in relation to diatom taxa suggesting the occurrence of several export modes to intermediate and deep layers within the diatom community. We observed a dominant contribution of single cell diatoms (93 ± 6%) to the deep particle stocks but a very small contribution of intact diatom cells (~0.3%) to C content in the intermediate layer (125–500 m), together with a very small fecal pellet contribution, that was dominated by the minipellet size-class. Taxonomical analyses revealed distinct communities west of Kerguelen in the HNLC area compared to the island's fertilized plateau and its eastern flank. Differences in silicification degrees as well as distinct mortality/export processes linked to surface nutrient depletion and trophic interactions (such as parasitic infection or grazing by phaeodarians) were identified in the upper layer, leading to distinct contributions of major diatom taxa to deep suspended particles.