Hyperthermophilic archaea are facing severe challenges due to their high temperature environment. Therefore, how to maintain genomic stability of hyperthermophilic archaea is one of the most important scientific questions in this field. Hyperthermophilic archaea have similar spontaneous mutation frequencies to mesophilic microorganisms, suggesting that they have a more efficient DNA repair system than mesophilic microorganisms to repair genomic DNA damage caused by high temperature. At present, the molecular mechanism of DNA repair of hyperthermophilic archaea is still unclear. Endonucleases play an important role in the DNA repair pathway. Genomic sequences show that hyperthermophilic archaea encode a few DNA repair endonucleases, however, the research on them is still in an early stage. In this paper, we reviewed the research progress of hyperthermophilic archaeal DNA repair endonucleases, including NucS, EndoV, EndoQ, XPF and Hjc. We also proposed future studies.