The significant contribution of bacteria involved in the anammox (anaerobic ammonium oxidation) process to the global N cycle is becoming apparent through studies in marine and freshwater sediments and water columns. First discovered in a wastewater treatment plant, anammox bacteria are thought to be widespread in the environment, although the extent of their activity in many habitats is unknown. Unlike denitrification, anammox is an anaerobic, primarily autotrophic process that converts ammonium and nitrite to dinitrogen gas and is responsible for up to 70% of N losses in marine sediments. Here we report on the quantitative linkage between the anammox process and the catalyst in deep marine sediments using a combination of 16S based Q-PCR assays and  ¹⁵N-tracer studies. The tight coupling between anammox abundance and activity (R²=0.93) provides an assessment of potential activity in these types of sediments using a high-throughput, less costly assay. With this strong relationship in mind, anammox abundance in freshwater sediments is explored using 16S-based Q-PCR for the Candidatus “freshwater” anammox. This is linked to cell-based activities in the literature to establish estimates of anammox activity within freshwater systems. Lastly, we report on the use of the 454 sequencing technology in attempts to identify specific anammox genera within sediments using newly designed 16S primers. With the development of these molecular tools we are now able to pose questions pertaining to the importance of the anammox process in agricultural systems and to the potential effects of fertilizer regimes on anammox metabolism.