Biofuels have been attracting increasing attention to provide a solution to the problems of climate change and our dependence on limited fossil oil. During the last decade, metabolic engineering has been performed to develop superior microorganisms for the production of so called advanced biofuels. Among the advanced biofuels, hydrocarbons possess high-energy content and superior fuel properties to other biofuels, and thus have recently been attracting much research interest. Here we review the recent advances in the microbial production of hydrocarbon fuels together with the metabolic engineering strategies employed to develop their production strains. Strategies employed for the production of long-chain and short-chain hydrocarbons derived from fatty acid metabolism along with the isoprenoid-derived hydrocarbons are reviewed. Also, the current limitations and future prospects in hydrocarbon-based biofuel production are discussed.