In this comparative study, direct conversion of algal biomass into biodiesel using supercritical methanol (SCM) and microwave-assisted (MW) transesterification methods was investigated. Wet algal biomass was used as feedstock in the supercritical methanol process and dry algal biomass for the microwave-assisted transesterification. Experimental runs were designed using a response surface methodology and the process parameters such as wet/dry algae to methanol ratio, reaction temperature, reaction time and catalyst concentrations were optimized for both processes. The microwave-assisted approach improves extractions of algae significantly, with a higher efficiency, reduced extractive-transesterification time and increased yield. While the non-catalytic supercritical methanol method produces highly purified extracts (free of harmful solvents and catalyst residues), and reduces energy consumption in separation and purification steps. The algal biodiesel samples from SCM and MW processes were compared using FT-IR and TGA analysis methods to identify the functional group attributions and thermal stability of the biofuel samples, respectively. The transmission electron microscopy (TEM) analysis of algal biomass and lipid extracted algae (LEA) and energy requirements for the two processes are also presented. (C) 2012 Elsevier Ltd. All rights reserved.