Abstract: Nitrifying bacteria are one of the key functional groups in microbial nitrogen removal, and the screening of high-quality nitrifying bacteria is beneficial to enhancing nitrogen removal. The functions of nitrifying bacteria from river sediment, soil natural environment and artificial habitat in the market were compared, and their community structures were analyzed using molecular biological methods. The results showed that the activities of nitrifying bacteria from the sediment habitat and their resistance abilities to ammonia nitrogen, pH and salinity were higher than those from the other two habitats. The abundance and community structure analysis of nitrifying bacteria in each habitat by MPN-PCR and clone library profiling showed that the biomass of Nitrospira in the sediment habitat was high, which could promote the ammonia nitrogen removal rate of nitrifying bacteria in this habitat. For sediment nitrifying bacteria, the higher resistance to ammonium and pH was due to the presence of Nitrobacter, while the higher resistance ability to salinity was possibly due to the presence of salt-tolerant species or moderately halophilic specific genotypes of nitrifying bacteria in the habitat. In addition, these specific genotypes of nitrifying bacteria were identified as uncultured microbes by sequence alignment by Blast program.