Algae based third generation biodiesel production is a recent advancement in renewable energy due to its minimal land requirements, cultivation in wastelands etc than food stock based second generation biodiesel production. This paper addresses on the study the optimum yield of biodiesel produced from oxygenic photosynthetic bacteria-based Spirulina Platensis algae by microwave assisted transesterification. Effect of microwave irradiation time which affects the temperature on the extraction of algal oil and simultaneous in-situ transesterification was investigated for biodiesel production. The response surface methodology using Box Behnken Design was used to analyze constituent parameters like catalyst concentration, alcohol concentration and process parameters like microwave time. Results indicate that microwave assisted transesterification produces 71.7% of biodiesel with respect to algae dry weight at catalyst concentration of 1.6%, with alcohol concentration of 1:9.7 and microwave irradiation time of 3.2 minutes