Nitrogen cycle is a biogeochemical cycle mediated by both abiotic and biotic processes. The important research hotspot in environmental genomics and microbial ecology is to use gene sequencing technology to study microbial communities, microorganisms and functional genes involved in the nitrogen cycle in the environment. In recent years, various types of databases are developed and applied to functional analysis. Combining with the latest research results, we focus here on the functional genes of six inorganic nitrogen cycle pathways driven by microorganisms, containing assimilation nitrate reduction, dissimilation nitrate reduction, denitrification, nitrogen fixation, nitrification (including complete ammonia oxidation) and anaerobic ammonia oxidation. we compare the design concepts and functional characteristics of databases such as National Center for Biotechnology Information (NCBI), Integrated Microbial Genomes (IMG), Universal Protein (UniProt), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein Families (Pfam), Functional Gene (FunGene), Clusters of Orthologous Groups (COG) and NCycDB. Also, we statistically analyze the selection and application of the above databases in the annotation of nitrogen cycle functional genes, combining with the influence factors such as environmental media, characteristic genes, analysis methods and comparison methods, and prospected the future development direction of the nitrogen cycle gene databases. It is expected to provide reference for researchers to understand the nitrogen cycle gene family and choose an appropriate data analysis platform.