With the development of urbanization and the highly intensified agriculture in the world, the massive anthropogenic loading of particular nitrogen compounds into rivers, and the environmental quality of many estuarine ecosystems in China are deteriorating through eutrophication. Ammonia oxidation, which is regulated by ammonia monooxygenase (AMO), is the critical and rate-limiting step in the nitrification. The diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) containing AMO encoded by the amoA gene can be impacted by environmental factors. Transformation and removal of the land-accumulated nitrogen in estuarine ecosystems could significantly reduce eutrophication. The steep physico-chemical gradients in estuary linking freshwater, terrestrial and marine systems serve as an important natural laboratory for studying ammonia-oxidizing microorganisms. Previous studies have reviewed the characteristics of AOA and AOB composition, their abundance, and nitrification levels in the estuarine ecosystems, as well as their responses to environmental factors. There are strong correlations between the ammonia oxidizers' diversity and environmental parameters,e.g. salinity, eutrophication, vegetation, temperature, carbon, nitrogen, sulphur and iron in estuarine ecosystems, especially in salinity and eutrophication. Future directions and work of ammonia oxidizers with estuary ecosystems in China should be focused on as follows: (1) set up effective assessment method of nitrification induced by ammonia-oxidizers; (2) elucidate which kind of assimilation style, heterotrophic, autotrophic or mixotrophic is characteristic of AOA; (3) confirm that ammonia-oxidizer compositions could be used as biological indicators to indicate the environmental quality in estuaries; (4) cultivate and identify the most biologically effective ammonia-oxidizers from estuaries by combining traditional cultivation methods with modern molecular biotechnology techniques, and finally apply them to practical production.