Research findings of the past few decades on the cultivation of microalgae for biodiesel production from laboratory to pilot scale microalgal cultivation have translated into empirical hope of developing an eco-friendly biofuel from algae. As far as economic sustainability is concerned, harvesting of microalgae is one of the most energy extensive processes and thus a major challenge, being faced by this industry. In our study, we designed and developed a quaternary ammonium salt based cationic polymer and evaluated its effectiveness for freshwater microalgae harvesting. An epichlorohydrin-n,n-diisopropylamine-dimethylamine polymer with high viscosity (1040 cps) was synthesized. The flocculation performance of this polyamine polymer was evaluated in terms of biomass recovery efficiency of microalgae (Scenedesmus sp.), its effect on lipid yield and composition. The results revealed that due to high molecular weight, the biomass recovery efficiency of the polymer was achieved >90% at a very small dose of 8 mg/L whereas similar biomass recovery efficiency of chitosan and alum were achieved at 80 and 250 mg/L respectively. The presence of functional quaternary amine and hydroxyl groups played an important role in electric charge neutralization of microalgal cells, hence the improved microalgal flocculation performance in comparison to the natural flocculants but not affecting the lipid yield and its composition. The approximate cost of harvesting 1 kg of Scenedesmus biomass is approximately 0.5 USD for the polyamine polymer whereas 50 USD for chitosan. Therefore, polymer based harvesting of microalgae for low valued products such as biodiesel, polyamine based polymers would be preferred over the natural polymer. (C) 2014 Elsevier Ltd. All rights reserved.