Both NRT36S and A5 are NAG-ST-producing, serogroup O31 Vibrio cholerae. NRT36S is encapsulated and causes diarrhea when administered to volunteers; A5 is unencapsulated and does not colonize or cause illness in humans. The capsule/LPS (CPS/LPS) biogenesis regions in these two isolates were similar except that a 6.5-kb fragment in A5 has replaced a 10-kb fragment in NRT36S in the middle of the CPS/LPS gene cluster. Although the genes of the replaced region were homologous to genes from other CPS/LPS, they had little similarity to NRT36S and were not homologous to genes from other Vibrios. Data of this study highlight the apparent mobility within the CPS/LPS region that would provide a basis for the large number of observed V. cholerae serogroups and the emergence of novel epidemic strains.