The anthropogenic nitrogen (N) input as an important source strongly influences the microbial N cycling in coastal ecosystems. In this study, we investigated the responses of anammox bacteria, ammonia oxidizing archaea (AOA), and ammonia oxidizing bacteria (AOB) to the amendments of ammonium and nitrite into mangrove sediments incubated in laboratory microcosm experiments. The variations of diversity, abundances, and transcription of 16S rRNA and hydrazine oxidoreductase (hzo) genes for anammox bacteria, and amoA genes for AOA and AOB were monitored during the incubation. The T-RFLP analysis demonstrated that both ammonium and nitrite additions significantly altered the community compositions of anammox bacteria, AOA, and AOB, while abundance and transcripts analyzed quantitatively confirmed that the amendment of ammonium (25 mM) stimulated the growth of anammox bacteria, AOA, and AOB, whereas nitrite (0.8 mM) generally inhibited them with some exceptions for specific species of AOA and AOB, showing different responses of anammox bacteria, AOA, and AOB to the nitrite and ammonium amendments. Results further suggest that AOB as the dominant group with higher amoA gene abundances and transcripts might play a more important role on the ammonium oxidization in mangrove sediment of this subtropical site.