Diatoms play a major role in carbon export from surface waters, but their role in the transport of carbon to the deep sea has been questioned by global analyses of sediment trap fluxes which suggest that organic carbon fluxes and transfer efficiencies through the mesopelagic are tightly correlated with CaCO3 ( Klaas and Archer, 2002; Franc, ois et al., 2002). Here we explore the role of diatoms in the biological pump through a study of Si and C interactions from the molecular to the global scale. Recent findings on molecular interactions between Si and C are reviewed. The roles of bacteria, grazers and aggregation are explored and combined, to account for the extent of Si and C decoupling between surface waters and 1000 m, observed to be very homogeneous in different biogeochemical provinces of the ocean. It is suggested that the mesopelagic food web plays a crucial role in this homogeneity: Sites of high export are also sites where diatom C is being either remineralized or channeled toward the long-lived carbon pool most efficiently in the mesopelagic zone. The amount of carbon participating in the biological pump but not collected in sediment traps remains to be explored. It is also demonstrated that statistical analyses performed at global scales hide spatial variability in carrying coefficients, indicating a clear need to understand the mechanisms that control spatial and temporal variations in the relative importance of ballast minerals and other export mechanisms such as particle dynamics.