The respiratory reduction of nitrate (denitrification) is acknowledged as the most important process that converts biologically available nitrogen to gaseous dinitrogen (N2) in marine ecosystems. Observations during the last decade, however, indicate that anaerobic ammonium oxidation by nitrite (anammox) may be an important pathway for N2 formation and N removal in coastal marine sediments and in anoxic water columns of the oceans (e.g. Hulth et al., 2005). For about a decade we have explored this mechanism during N mineralization by a wide range of biogeochemical and molecular tools including e.g. benthic flux measurements and high resolution imaging of solute distributions, 15N amendments (single and coupled additions of 15NH4+, 14NO3- and 15NO3-), polymerase chain reaction (PCR), and qualitative and quantitative fluorescence in situ hybridization (FISH) (e.g. Brandsma et al., 2011 Schmid et al., 2007 Engstrom et al., 2005 Jetten et al., 2003). The present study focuses on benthic N-cycling in the deepest trough of a Swedish fjord where the anammox reaction contributes up to 79% of total N2 production. The relative importance of anammox for N2 release was directly correlated with a variety of biogeochemical parameters. The observed correlations indicated a competition between reductants for pore water nitrite during early diagenesis, and that additional factors (e.g. availability of Mn-oxides), superimposed on overall patterns of diagenetic activity, are important for determining absolute and relative rates of anammox in coastal marine sediments. Insight in the metagenome of the microbial community in this complex benthic environment would provide complementary and critical information to further understand N cycling in marine environments.