In this comparative study, the direct conversion of algal biomass to biodiesel using the supercritical methanol and the microwave-assisted 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. It was observed that both conversion techniques have the potential to provide energy-efficient routes for biodiesel production from algal biomass. In comparison, the microwave-assisted approach was more successful in extracting majority of the polyunsaturated fatty acids and other valuable byproducts from the algal biomass in a short period of reaction time; and the non-catalytic supercritical methanol process may reduce the energy consumption due to easier separation and purification steps. The algal biomass characterization and algal biodiesel analysis using ATR-FTIR and GC-MS methods are reported. The transmission electron microscopy (TEM) analysis, fatty acid composition and energy requirements for the two processes are also presented.