The hyperthermophilic Archaea are the most extreme extremophiles in terms of temperature, some grow optimally at temperatures >100C. Many of the hyperthermophilic Archaea (defined as having optimal growth temperatures >80C) are also acidophiles (optimal growth at pH < 3). The best studied of these are the Sulfolobales, for which three complete genome sequences are available. Sulfolobus and related organisms are dominant in thermophilic bio-leaching reactors and acidic volcanic hot springs, and show considerable promise in bio-remediation. Recently a number of genetic tools have been made for the study of Sulfolobus solfataricus. One of these is a gene-knockout system, allowing specific gene disruption in the chromosome. On the other hand a number of plasmids and viruses of Sulfolobus have been described. One of these, the virus SSV1, has a novel morphology and a double stranded circular genome with unique content. We and our collaborators have used this virus to make three generations of infectious shuttle vectors for complementation, heterologous gene expression, and gene expression studies. Very recently we developed a long-inverse PCR method to make specific mutations in the SSV1 virus genome. This allowed very precise mutagenesis and characterization of the viral integrase gene. A combination of these genetic tools together with new isolates should stimulate the use of these organisms and their viruses in not only basic research, but also bio-leaching and bio-remediation.