Bacteroides are Gram-negative, obligate anaerobes that are present in high concentrations within the intestinal tracts of humans and animals. Bacteroides are also important opportunistic pathogens of humans and animals. Methods for genetic manipulation of these important organisms have only recently begun to emerge. Shuttle vectors which can be transferred by conjugation between Escherichia coli to Bacteroides are now available. A method for transforming some strains of Bacteroides has been developed. Two Bacteroides transposons, Tn4351 and Tn4400, have been found and one of them, Tn4351, has been used for transposon mutagenesis of Bacteroides. Several different Bacteroides genes have now been cloned, including a gene that codes for resistance to clindamycin, genes that code for polysaccharidases (chondroitin lyase and pullulanase), and a gene that codes for a fimbrial subunit. These cloned genes have been used to study the organization and regulation of Bacteroides genes.