Organisms of the genus Bacteroides are part of the indigenous microbiota of the human and animal gastrointestinal tract, but different species in this group are commonly associated with a variety of human and animal infections. The genus Bacteroides is an important bacteria group in clinical bacteriology. In the past, because of poor definition of the genus, more than 50 species of Bacteroides have been included in this group. The taxonomy of the genus Bacteroides has undergone significant changes in the past few years. Recently, the application of molecular-biological techniques without cultivation revealed that there were large numbers of as-yet-to-be-cultured organisms that should be classified as species of the genus Bacteroides and related taxa in the human oral cavity or gastrointestinal tract. In this review, the recent classification of the genus Bacteroides and related taxa are discussed.