The DNA sequences of the asd genes from 45 isolates of Vibrio cholerae (19 clinical O1 isolates, 2 environmental nontoxigenic O1 isolates, and 24 isolates with different non-O1 antigens) were determined. No differences were found within either sixth-or seventh-pandemic isolates; however, variation was found between the two forms and among the non-O1 isolates. O139 isolates had sequences identical to those of seventh-pandemic isolates. Phylogenetic trees with Vibrio mimicus as the outgroup suggest that the sixth-pandemic, seventhpandemic, and U.S. Gulf isolates are three clones that have evolved independently from different lineages of environmental, nontoxigenic, non-O1 V. cholerae isolates. There is evidence for horizontal transfer of O antigen, since isolates with nearly identical asd sequences had different O antigens, and isolates with the O1 antigen did not cluster together but were found in different lineages. We also found evidence for recombination events within the asd gene of V. cholerae. V. cholerae may have a higher level of genetic exchange and a lower level of clonality than species such as Salmonella enterica and Escherichia coli.Vibrio cholerae is a normal inhabitant of aquatic environments (46). However, contaminated water supplies in some areas of the world have enabled some clones of the species to become pathogenic for humans. Seven pandemics of cholera have been recorded previously (12,36). The seventh pandemic, beginning in 1961, is clonal (20,22,24,37), is well defined, and has a known starting date, and previous studies (7,22,24,37,53) have shown it to have accumulated variation, with both random genetic drift and recombination possibly being involved. There are 140 known serotypes of V. cholerae (50). Until recently, all recorded pandemic and epidemic cases of cholera have been associated with the type O1 antigen; however, an epidemic which began in India late in 1992 and spread to several neighboring countries is caused by an O139 strain (1,8,33,39). Studies have shown that the O139 strain is genetically very similar to strains of the seventh pandemic (13,22,37,54). Karaolis et al. (22) have further shown that O139 isolates appear to have evolved from early seventh-pandemic isolates. Biochemically, it is nearly impossible to distinguish O1 and non-O1 V. cholerae (10,38). V. cholerae non-O1 strains are far more frequently isolated from environmental sources than O1 strains and appear to constitute part of the normal microflora of prawns (31) and oysters (2,4,28,47). Most environmental isolates do not possess cholera toxin genes, a heat-stable enterotoxin (31, 32), or toxin coregulated pilus (49, 54).The population structure and molecular evolution of V. cholerae as a species have not been well characterized, and the relationship of the sixth-and seventh-pandemic isolates is not clear. We have investigated sequence variation within V. cholerae by examining variation in the asd locus, one of the few V. cholerae chromosomal housekeeping genes sequenced to date. Housekeeping genes are conce...