Objective To understand the genetic structures and variations of the superintegron (SI) in Vibrio cholerae isolated in the seventh cholera pandemic.Methods Polymerase chain reaction scanning and fragment sequencing were used.Sixty toxigenic V.cholerae O1 EI Tor strains isolated between 1961 and 2008 were analyzed.Results Some variations were found,including insertions,replacements,and deletions.Most of the deletions were probably the result of recombination between V.cholerae repeat sequences.The majority of the variations clustered together.The Sls of the strains isolated in the 1960s and 1970s showed more diversity,whereas SI cassette variations in strains isolated in the 1990s and after were lower,with ～24 kb signature sequence deletion.This indicates the predominant Sl in the host during the epidemic in the 1990s and after.The insertion cassettes suggested the mobilization from the Sls of other Ⅴ.cholerae serogroups and Vibrio mimicus.Conclusion The study revealed that structural variations of Sls were obvious in the strains isolated in epidemics in different decades,whereas the divergence was based on syntenic structure of Sls in these El Tor strains.Also,the continuing cassette flows in the Sls of the host strains during the seventh cholera pandemics were displayed.