The sinking of particulate organic matter from ocean surface waters transports carbon to the ocean interior, where almost all is then recycled. The unrecycled fraction of this organic matter can become buried in ocean sediments, thus sequestering carbon and so influencing atmospheric carbon dioxide concentrations. The processes controlling the extensive biodegradation of sinking particles remain unclear, partly because of the difficulty in resolving the composition of the residual organic matter at depth with existing chromatographic techniques. Here, using solid-state 13C NMR spectroscopy, we characterize the chemical structure of organic carbon in both surface plankton and sinking particulate matter from the Pacific Ocean and the Arabian Sea. We found that minimal changes occur in bulk organic composition, despite extensive (>98%) biodegradation, and that amino-acid-like material predominates throughout the water column in both regions. The compositional similarity between phytoplankton biomass and the small remnant of organic matter reaching the ocean interior indicates that the formation of unusual biochemicals, either by chemical recombination or microbial biosynthesis, is not the main process controlling the preservation of particulate organic carbon within the water column at these two sites. We suggest instead that organic matter might be protected from degradation by the inorganic matrix of sinking particles.