Salinity is an important factor affecting the activity and community structure of nitrogen transformation related microorganisms in natural and engineered ecosystems. However, salinity's impact on microbial diversity in completely autotrophic nitrogen removal over nitrite (CANON) processes remains poorly described. In this study, the microbial community dynamic of a CANON system was comprehensively evaluated in response to increasing salt stress using 16S rRNA gene high-throughput sequencing technology. The CANON system can treat ammonia-rich (200 mg/L) wastewater with salinity up to 15 g NaCl/L after gradual acclimation to salt, and the maximum total nitrogen removal rate achieved was 0.23 kg/m(3)/d at 10 g NaCl/L. Salinity of 20 g NaCl/L caused rapid deterioration of the nitrogen removal performance because of a sharp decline in the ammonia oxidation rate. Beta diversity with elevated salinity by redundancy analysis proved that salinity played an important role in the microbial community dynamics of the functional microbes in the CANON system. "Candidatus Kuenenia" anaerobic ammonia oxidation (anammox) bacteria and "Nitrosomonas europaea" ammonia oxidation bacteria were robust under salt stress and could survive at salinity up to 15 g NaCl/L, while "Candidatus Jettenia" anammox bacteria were sensitive to salinity and even 5 g NaCl/L caused a sharp decline in their abundance. The nitrite oxidation rate showed extreme sensitivity to 5 g NaCl/L salinity; however, overgrowth of "Nitrospira" nitrite oxidation bacteria" even at elevated salinity is a matter of concern for successful CANON operation. 16S rRNA gene high-throughput analyses offer new insights at high resolution and depth into the stability and dynamics of functional microbial communities in CANON systems under increasing salt stress, highlighting the importance of microbial diversity and balance in the CANON process. (C) 2017 Elsevier B.V. All rights reserved.