Microalga Botryococcus braunii produces and stores liquid hydrocarbons. The oil extraction residue of the microalga is a good substitution for anaerobic digestion. However, hexane used as extraction solvent inhibits anaerobic digestion. In this study, the degree of inhibition from hexane and carbohydrate were measured in the continuous experiments. It was found that the hexane concentration and the remained carbohydrate should be kept under upper limits for success of the anaerobic digestion.