Since the industrial revolution, environmental contamination has increased, resulting in discharge of different types of industrial wastewaters with varying loads of organic and inorganic matter. Since the type of organic and inorganic compounds in wastewaters vary depending on the processes, different strategies need to be employed to remove them. The presence of inorganic nitrogenous compounds in wastewater is an environmental concern and the biological removal requires specific group of microorganisms, viz., nitrifying and denitrifying microorganisms. The metabolic activities of nitrifying (-ammonia oxidizing and -nitrifying microorganisms) and denitrifying microorganisms are interrelated and this interaction plays an important role in nitrogen cycle and N removal. In recent years, molecular analysis has aided in studying the abundance of specific microorganisms, their diversity, distribution, and identification of metabolic pathways. Furthermore, molecular tools have helped to identify biomarkers to monitor the activity of specific group of microorganisms, such as ammonia-oxidizing bacteria. This chapter summarizes the role of ammonia-oxidizing microorganisms in N cycle, their nitrifier/denitrification capacity, genetic regulation, and biomarkers related to this microbial activity.