Major progress in sequencing the genome of Sulfolobus solfataricus has been closely concerted with the characterization and sequencing of many extrachromosomal genetic elements, including viruses, cryptic plasmids and conjugative plasmids, as well as mobile archaeal introns and transposons. The rafter have provided a basis for developing the first generation of vectors that are now being used to study the genetics of Sulfolobus and other Archaea.