In recent years, microalgae have been investigated as a substitute for conventional fuels by many scholars and researchers of all over the world. Microalgae possess a hard cell wall that prevents intercellular lipids to get out of it. In situ transesterification has potential to interact with hard cell wall for the extraction of biodiesel at low energy consumption. In this study Response Surface Methodology was employed to investigate different parameters viz. methanol-to-dry-algae ratio, catalyst concentration, temperature and reaction time in order to attain high FAMEs from hydrodictyon microalgae. The present study is focused on a low temperature transesterification process for the better energy efficiency during the process. Experiments (17-17 each) were performed in a batch reactor for both acid (H2SO4) and base (NaOH) catalyst. A maximum biodiesel yield of 89.583% was achieved with methanol-to-dry-algae ratio (8:1, w/w), catalyst concentration (3.361%, w/w) in 60.443 min at 50 degrees C temperature for H2SO4 catalyst. On the other hand the maximum output yield of 87.421% was found with methanol-to-dry-algae ratio (8:1, w/w), catalyst concentration (3.499%, w/w) at 50 degrees C in 73.637 min of reaction time for NaOH catalyst.