Decomposition of organic matter in marine sediments is a critical step influencing oxygen and carbon fluxes. In addition to heterotrophic bacteria and fungi, osmoheterotrophic protists may contribute to this process, but the extent of their role as decomposers is still unknown. Among saprophytic protists, the thraustochytrids have been isolated from different habitats and substrates. Recently, they have been reported to be particularly abundant in marine sediments characterized by the presence of recalcitrant organic matter such as seagrass and mangrove detritus where they can reach biomass comparable to those of other protists and bacteria. In addition, their capacity to produce a wide spectrum of enzymes suggests a substantial role of thraustochytrids in sedimentary organic decomposition. Moreover, thraustochytrids may represent a food source for several benthic microorganisms and animals and may be involved in the upgrading of nutrient-poor organic detritus. This chapter presents an overview on studies of thraustochytrids in benthic ecosystems and discusses future prospectives and possible methods to quantify their role in benthic food webs.