Microalgae as a candidate for production of biodiesel, possesses a hard cell wall that prevents intracellular lipids leaving out from the cells. Direct or in situ supercritical transesterification has the potential for destruction of microalgae hard cell wall and conversion of extracted lipids to biodiesel that consequently reduces the total energy consumption. Response surface methodology combined with central composite design was applied to investigate process parameters including: Temperature, Time, Methanol-to-dry algae, Hexane-to-dry algae, and Moisture content. Thirty-two experiments were designed and performed in a batch reactor, and biodiesel efficiency between 0.44% and 99.32% was obtained. According to fatty acid methyl ester yields, a quadratic experimental model was adjusted and the significance of parameters was evaluated using analysis of variance (ANOVA). Effects of single and interaction parameters were also interpreted. In addition, the effect of supercritical process on the ultrastructure of microalgae cell wall using scanning electron spectrometry (SEM) was surveyed. (C) 2017 Elsevier Ltd. All rights reserved.