Hydrogen is noted widely because it is a clean energy. Many countries in the world are studying and developing new methods for hydrogen production. Biological hydrogen production is one of such new methods with the advantages of utilizing renewable energy and wastes, and of low cost. In this paper, the characteristics of 5 modes of biological hydrogen production were summarized and compared according to hydrogen metabolic energetic. Furthermore, the molecular mechanism of biological hydrogen production by anoxygenic phototrophic bacteria was described. Finally, the newest progress of hydrogen production by anoxygenic phototrophic bacteria in the aspects of electronic donor, coupling to light energy, inhibition of ammonium, and genetic manipulation and exploiting of application system was reviewed. Fig 1, Tab 1, Ref