Nitrogen removal characteristics and the comparison of the microbial community structure were investigated in different anaerobic ammonia oxidation (Anammox) reactors: an anaerobic sequencing batch reactor (ASBR) and a biofilter reactor. The Anammox systems were inoculated with sludge from the second settling tank of a wastewater treatment plant in Guangzhou, China. After successful start up of Anammox, the microbial community structure of different Anammox reactors were studied through high-throughput sequencing. The results showed that anaerobic ammonium oxidation in the ASBR reactor could successfully start up after 134 days, while Anammox in the biofilter could start up after 114 days. In both systems, total nitrogen removal was at 80% after more than 200 days of operation. The diversity of denitrifying microorganisms was high in both reactors, with Planctomycetes as the main taxa. Anammox bacteria belonging to the genera Candidatus Anammoxoglobus and Kuenenia, were dominant in the ASBR, while all three genera of Candidatus, Anammoxoglobus, Kuenenia, and Brocadia, could be detected in the biofilter reactor. Therefore, the biofilter starts up faster than the ASBR, and contains richer species, which makes it more suitable to domesticate Anammox bacteria.