The current global energy situation has demonstrated an urgent need for the development of alternative fuel sources to the continually diminishing fossil fuel reserves. Much research to address this issue focuses on the development of financially viable technologies for the production of biofuels. The current market for biofuels, defined as fuel products obtained from organic substrates, is dominated by bioethanol, biodiesel, biobutanol and biogas, relying on the use of substrates such as sugars, starch and oil crops, agricultural and animal wastes, and lignocellulosic biomass. This conversion from biomass to biofuel through microbial catalysis has gained much momentum as biotechnology has evolved to its current status. Extremophiles are a robust group of organisms producing stable enzymes, which are often capable of tolerating changes in environmental conditions such as pH and temperature. The potential application of such organisms and their enzymes in biotechnology is enormous, and a particular application is in biofuel production. In this review an overview of the different biofuels is given, covering those already produced commercially as well as those under development. The past and present trends in biofuel production are discussed, and future prospects for the industry are highlighted. The focus is on the current and future application of extremophilic organisms and enzymes in technologies to develop and improve the biotechnological production of biofuels.