Despite the increased interest in hyperthermophiles and the rate of discovery of new species, their potential within the biotechnology industry has not been fully realized to date. The physiological characterization and biochemical survival mechanisms of marine hyperthermophilic Bacteria and Archaea are currently under investigation. However, very little information on their application in bioprocess systems is available. Since only a fraction of the world's oceans has been explored, the potential for isolating novel strains of marine hyperthermophiles is significant and hence they represent an, as yet, untapped biotechnological resource. Although much research has focused on the extraction of thermoactive enzymes, whole cell applications have been relatively overlooked. Running bioprocess systems using marine hyperthermophiles poses an interesting set of objectives, such as high temperature bioreactor operation and corrosion reduction of materials, for bioreactor design and manipulation of their products. Here, we discuss the biotechnological potential of marine hyperthermophiles from a biochemical engineering perspective and their use in 'green chemistry' applications. Both the bioprocess intensification implications and problems associated with cultivating these microbes in industrially relevant bioreactor systems are discussed from both a microbiological and chemical engineering perspective.