Biogas production is one of the means to produce a biofuel from microalgae. Biomass consisting mainly of Scenedesmus sp. was thermally pretreated and optimum pretreatment length (1 h) and temperature (90 °C) was selected. Different chemical composition among batches stored at 4 °C for different lengths of time resulted in organic matter hydrolysis percentages ranging from 3% to 7%. The lower percentages were attributed to cell wall thickening observed during storage for 45 days. The different hydrolysis percentages did not cause differences in anaerobic digestion. Pretreatment of Scenedesmus sp. at 90 °C for 1h increased methane production 2.9 and 3.4-fold at organic loading rates (OLR) of 1 and 2.5 kg COD m(-3) day(-1), respectively. Regardless the OLR, inhibition caused by organic overloading or ammonia toxicity were not detected. Despite enhanced methane production, anaerobic biodegradability of this biomass remained low (32%). Therefore, this microalga is not a suitable feedstock for biogas production unless a more suitable pretreatment can be found.