The relationships within a curated set of 112 insertion sequences (ISs) currently assigned to the IS family, here re-named the IS/IS family, in the ISFinder database were examined. The encoded DDE transposases include a helix-helix-turn-helix (H-HTH) potential DNA binding domain N-terminal to the catalytic (DDE) domain, but 10 from include one or two additional N-terminal domains. The transposase phylogeny clearly separated 75 derived from bacteria from 37 from archaea. The longer bacterial transposases also clustered separately. The 65 shorter bacterial transposases, including Tnp26 from IS, formed six clades but share significant conservation in the H-HTH domain and in a short extension at the N-terminus, and several amino acids in the catalytic domain are completely or highly conserved. At the outer ends of these ISs, 14 bp were strongly conserved as terminal inverted repeats (TIRs) with the first two bases (GG) and the seventh base (G) present in all except one IS. The longer bacterial transposases are only distantly related to the short bacterial transposases, with only some amino acids conserved. The TIR consensus was longer and only one IS started with GG. The 37 archaeal transposases are only distantly related to either the short or the long bacterial transposases and different residues were conserved. Their TIRs are loosely related to the bacterial TIR consensus but are longer and many do not begin with GG. As they do not fit well with most bacterial ISs, the inclusion of the archaeal ISs and the longer bacterial ISs in the IS/IS family is not appropriate.