Botryococcus braunii is a colonial microalga that produces hydrocarbons. While the microalga stores almost all the amount of hydrocarbons in its colony matrix, the amount of the extracted hydrocarbon without any pretreatment is typically very small. We performed mechanical cell disruption using a JET PASTER (R) and a bead mill as the pretreatment ways to facilitate hydrocarbon extraction from B. braunii. After the disruption, the size and shape of colonies changed. In the JET PASTER treatment at 4800 rpm, the concentration of removed polysaccharides increased 146 to 173 mu g/mL and the hydrocarbon yield increased 2.7 to 82.8%. In the bead mill treatment, the concentration of removed polysaccharides increased 146 to 210 mu g/mL and hydrocarbon yield increased 2.7 to 42.3%. Therefore, the disruption of colonies and polysaccharides around algal colonies would affect the hydrocarbon extraction. In addition, the apparent photosynthetic activity of the sample treated by the JET PASTER was 0.71 that is almost the same value as that of the untreated sample, whereas that of the sample treated by the bead mill was 0.64. Therefore, the JET PASTER treatment did not affect the photosynthetic function of B. braunii.