The present book describes and compares the phototrophic and mixotrophic cultivation of three microalgae species (Chlorella protothecoides, Chlorella vulgaris, Nannochloropsis oculata) in lab scale photobioreactor. in-situ transesterification of wet algal biomass (70% moisture) was conducted in low cost microwave reactor for all three species. A new route was adopted to produce biodiesel involving a series of steps :i) direct saponification of wet biomass ii) Precipitation of soaps iii) Simultaneous acidulation and esterification of fatty acids to produce biodiesel.The effect of various operating parameters on the yield of saponification such as microwave power, temperature, ethanol to dry biomass ratio and concentration of KOH was studied. The kinetics and thermodynamic studies were conducted for both saponification and esterification in microwave reactor.