In order to relieve the pressure of energy supply and environment contamination that humans are facing, there are now intensive worldwide efforts to explore natural bioresources for production of energy storage compounds, such as lipids, alcohols, hydrocarbons, and polysaccharides. Around the world, many plants have been evaluated and developed as feedstock for bioenergy production, among which several crops have successfully achieved industrialization. Microalgae are another group of photosynthetic autotroph of interest due to their superior growth rates, relatively high photosynthetic conversion efficiencies, and vast metabolic capabilities. Heterotrophic microorganisms, such as yeast and bacteria, can utilize carbohydrates from lignocellulosic biomass directly or after pretreatment and enzymatic hydrolysis to produce liquid biofuels such as ethanol and butanol. Although finding a suitable organism for biofuel production is not easy, many naturally occurring organisms with good traits have recently been obtained. This review mainly focuses on the new organism resources discovered in the last 5 years for production of transport fuels (biodiesel, gasoline, jet fuel, and alkanes) and hydrogen, and available methods to improve natural organisms as platforms for the production of biofuels.