The lack of knowledge on the fate of explosive compounds 2,4,6‐trinitrotoluene (TNT) and hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine (RDX), particularly in marine ecosystems, constrains the application of bioremediation techniques in explosive‐contaminated coastal sites. The authors present a comparative study on anaerobic biodegradation and mineralization of 15N‐nitro group isotopically labeled TNT and RDX in organic carbon–rich, fine‐grained marine sediment with native microbial assemblages. Separate sediment slurry experiments were carried out for TNT and RDX at 23°C for 16 d. Dissolved and sediment‐sorbed fractions of parent and transformation products, isotopic compositions of sediment, and mineralization products of the dissolved inorganic N pool (15NH4+,15NO3–,15NO2–, and 15N2) were measured. The rate of TNT removal from the aqueous phase was faster (0.75 h−1) than that of RDX (0.37 h−1), and 15N accumulation in sediment was higher in the TNT (13%) than the RDX (2%) microcosms. Mono‐amino‐dinitrotoluenes were identified as intermediate biodegradation products of TNT. Two percent of the total spiked TNT‐N is mineralized to dissolved inorganic N through 2 different pathways: denitration as well as deamination and formation of NH4+, facilitated by iron and sulfate reducing bacteria in the sediments. The majority of the spiked TNT‐N (85%) is in unidentified pools by day 16. Hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine (10%) biodegrades to nitroso derivatives, whereas 13% of RDX‐N in nitro groups is mineralized to dissolved inorganic N anaerobically by the end of the experiment. The primary identified mineralization end product of RDX (40%) is NH4+, generated through either deamination or mono‐denitration, followed by ring breakdown. A reasonable production of N2 gas (13%) was seen in the RDX system but not in the TNT system. Sixty‐eight percent of the total spiked RDX‐N is in an unidentified pool by day 16 and may include unquantified mineralization products dissolved in water. Environ Toxicol Chem 2017;36:1170–1180. © 2016 SETAC