Sediments can serve as sinks for hydrocarbon contaminants in marine ecosystems. Once settled, hydrocarbons fate will be dominated by several abiotic and biotic processes that will result in either their partial or total degradation or in a selective preservation when buried within the sediment. Biodegradation of hydrocarbons in marine sediments is mainly due to the existence of prokaryotes harbouring specific catabolic genes enabling the degradation of these compounds under oxic, suboxic and anoxic conditions. The interplay of the various factors that govern hydrocarbons biodegradation in marine sediments is highly complex as illustrated by bioturbation processes carried out by macrofaunal organisms. For instance, the redox oscillation regimes generated by macrofaunal organisms, and the efficiency of metabolic coupling between functional groups associated to these specific redox regimes, are probably determinant factors controlling the biodegradation rates of hydrocarbons in marine sediments. From the understanding of how these natural occurring factors may modulate the rates of hydrocarbons biodegradation, innovative bioremediation strategies may emerge.