The complete nucleotide sequences of two copies of a putative insertion sequence IS1000 fromThermus thermophilus HB8 are presented. IS1000 is 1196 base pairs long, contains a long open reading frame which could code for a protein of 317 amino acids, and has imperfect terminal inverted repeats of 6 base pairs (confirmed by the terminal sequencing of 4.5 copies of IS1000), but does not cause a target site duplication. There are at least 6 copies of IS1000 in the genome ofT. thermophilus HB8. A search of the GEN-EMBL data base revealed that the putative 317 ammo acid protein had significant homology with open reading frames in the transposable elements IS110 ofStreptomyces coelicolor and IS492 ofPseudomonas atlantica.