The integrative genetic elements involved in the spreading of virulence factors, defense and DNA modification, and secondary metabolism have been characterized in bacteria, but similar investigations on the function of the hyperthermophilic archaeal counterparts are still very rare. This review summarizes the reported groups of integrative genetic elements, the mechanism of integration and maintenance of such genetic elements in hyperthermophilic archaea. The horizontal gene transfer processes mediated by integrative genetic elements play important roles in the genome evolution of hyperthermophilic archaea. Functional genomic studies of integrative genetic elements provide a new perspective for understanding the diversity and environmental adaptability of hyperthermophilic archaea.