Anaerobes are the largest number of microorganisms on earth but rarely reported from the point view of taxonomy. Owing to oxygen-sensitive and slow-growth, cultivation and isolation of fastidious anaerobe faces a great challenge. In this review, we introduce the research history of anaerobes, and analyze the factors affecting the isolating efficiency of anaerobes. Furthermore, we discuss the current status of isolation and cultivation methods and strategies, and summarize the research progress on systematic taxonomy of anaerobes. In the end, we give an outlook for isolating and cultivating anaerobes.