The presence of Class II transposon genes related to Tn21 and Tn501, and their structural arrangements have been determined in a collection of 124 mercury resistant Gram-negative bacteria. Seventy-five of the 124 isolates contained a tnpA (transposase) gene related to Tn21 and Tn501 and in all 64 isolates that contained both tnpA genes and plasmids, the tnpA gene was plasmid borne. The relative orientation of the tnp genes and the mer operon (encoding mercury resistance) was also studied and revealed the presence of two distinct structural groups. The merC gene was present in 44 isolates. Five isolates were found to carry integrase genes and these contained inserted gene cassettes varying in size from 1.1 kb to 4.5 kb. The structural arrangement of the tnpA and tnpR (resolvase) genes within the isolates was determined. Sixty-nine of the 75 tnpA containing isolates had an arrangement of tnpA and tnpR genes similar to that found in the Tn21 subgroup of transposons. Four strains did not produce a PCR product using tnpR primers. The remaining two isolates had undetermined arrangements of tnpA and tnpR genes. No Tn3-like arrangements of tnpA and tnpR genes were present in these isolates, despite being detected in DNA extracted directly from the isolation sites. This suggests that Tn3-like arrangements of tnpA and tnpR genes are not commonly associated with mercury resistance genes in these environments. It was also apparent that the recombination events which have previously been observed in these strains have not significantly affected the diversity of the transposon structures within the isolates.