Methanotrophs are a fascinating group of bacteria that have the unique ability to grow on methane as their sole carbon and energy source. They appear to be widespread in nature and have been isolated from a number of different environments, including soils, sediments, freshwater, marine sediments, seawater, acid peat bogs, hot springs and cold environments such as the Antarctic. There are now eight recognised genera of methanotrophs. Methanotrophs have attracted a great deal of interest over the past 30 years since they have considerable potential for the production of bulk chemicals, fine chemicals and in bioremediation processes, such as the degradation of the groundwater pollutant trichloroethylene. More recently, they are being extensively studied in a wide variety of environments since methanotrophs play a critical role in the global methane cycle. Polymerase chain reaction-based methods have been used to study the ecology and diversity of methanotrophs. We review here molecular ecology methods that are already available or which are currently being developed for methanotrophs. These are based on 16S ribosomal RNA technology and specific amplification of ‘functional genes’, such as those encoding unique enzymes in the metabolism of these organisms including methane monooxygenase and methanol dehydrogenase.