Anoxygenic phototrophic bacteria (APB) are good model organisms used to study the origin and evolution of life, photosynthesis and nitrogen fixation mechanism. With increasingly available genetic information and establishment of sequencing techniques for nucleic acid, more attention has been paid to exploration of APB resources from various habitats especially extremely environment. The pace of new species description has been increasing in recent years, and some new taxonomic taxa are also proposed, therefore, it is necessary to redefine APB and provide the newest taxonomic system of APB. We reviewed the problems and prospect about taxonomy of anoxygenic phototrophic bacteria. The definition, situation of the taxonomy, characteristics for APB identification are noted and commented from the discovery of APB up to now.