A genomic fragment containing the insertion sequence ISC1041 has been cloned by PCR from the archaeon Sulfolobus solfaricus MT-4, an extremophilic microorganism which grows at 87 degrees C. The 1038 bp ISC1041 element contains an imperfect 18 nt repeat and a long open reading frame which encodes a polypeptide of 311 amino acid residues. The translated amino acid sequence shows a significant similarity to IS30-like transposases. Structural analysis indicates that ISC1041 is a novel member of the IS30 family and displays the DDE motif not previously seen in Archaea. This motif is believed to be involved in the integration mechanism of many mobile elements. As this motif is present in several integrases and transposases which, despite the lack of overall protein homologies, share topological homologies to the DDE motif, a common ancestor has been proposed. The finding of an IS30-like transposase in the archaeal kingdom may have relevance for horizontal gene transfer.