Picocyanobacteria Prochlorococcus and Synechococcus are the most abundant primary producers in the global ocean, yet their contribution to carbon export has long been overlooked. Based on surveys of picocyanobacterial abundance (by qPCR) and community structure along water-column profiles and sediment cores across the South China Sea and Indian Ocean, here we found that picocyanobacterial abundance were roughly 10–100 cells mL⁻¹ in deep waters, and up to 100000 cells g⁻¹ in surface sediments and 100 cells g⁻¹ at 800 cm below seafloor. Moreover, picocyanobacterial export and preservation were strongly lineage-specific: deep-water communities were mainly derived from surface Prochlorococcus lineages, whereas Synechococcus showed generally higher export efficiency and dominated sedimentary communities, especially clades 5.1-CRD1 and 5.1-I. Furthermore, we estimated that nearly 99% exported picocyanobacterial cells are decomposed in surface sediment. These results suggest that Prochlorococcus may contribute more to supplying organic matter for element recycling, whereas Synechococcus may have greater contribution to carbon sequestration.