Denitrification, a microbial process, is a major branch of the geography nitrogen cycle. Although the denitrifying ability has been widely found in bacteria, fungi and Archaea, the genes encoding the denitrifying reductases have been studied in few species. Modern molecular biology techniques provide effective methods to study the microbial ecosystem, and important knowledge has been accumulated on using functional genes for molecular techniques in the case of denitrification. Recent investigations on functional genes and molecular ecology in denitrifiers have been summarized.