Hyperthermophilic archaea are characterized with robust metabolic capability and outstanding enzyme stability. Since their discovery, great efforts have been devoted into the development of genetic tools for these archaea, and important progresses have been made in the past three decades including the development of conventional and novel genetic manipulation methods as well as CRISPR-based genome editing technologies. These genetic methods have enabled efficient genome engineering of these archaea, including engineering of promoter elements, highly efficient enzymes, as well as modified or new metabolic pathways for different biotechnological applications. Herein we summarize these research progresses in their genetic studies and bioprocessing efficiency and environmental sustainability of these hyperthermophilic and thermoacidophilic archaea, which provide the basis to generate environment-friendly and circular bioeconomies with these unique organisms.