Anaerobic ammonium oxidation (anammox) is a type of biological oxidation mediated by a group of Planctomycete-like bacteria. Members of the genus Candidatus Scalindua are mainly found in marine environments, but not exclusively. This group is cultured using different inoculums and conditions; however, its optimal growth conditions are not clear. Additionally, little information is known about the factors that influence the activity and the selection of a population of marine anammox bacteria. This study was conducted to investigate the influence of temperature and salinity on the marine anammox community. To accomplish this, an up-flow fixed-bed column reactor was operated, and quantitative fluorescence in situ hybridization (FISH) with probes specific to dominant marine anammox bacteria was conducted. Anammox activity was observed at 20 and 30 °C, but not at 10 °C. A nitrogen removal rate of 0.32 kg TN m(-3) day(-1) was obtained at 20 °C. These results suggest that temperature affects the activity (nitrogen removal rate) of anammox bacteria, while salinity does not affect the activity in the marine anammox biofilm.