Microalgae's potential to produce high value bioactives is contingent on the cost-effective harvesting of algal biomass. The use of CTAB (cetyl trimethylammonium bromide) assisted dispersed air flotation as a harvesting technique for Schizochytrium biomass, was optimized as a cost-effective means for recovery (R) and concentration factor (CF) using Response Surface Methodology. To the best of our knowledge, this is the first study to employ surfactant assisted dispersed air flotation (SDAF) in the recovery of a heterotrophic thraustochytrid strain. A Box-Behnken design of experiment investigating the operating parameters of CTAB amount, air flow rate and volume on Schizochytrium was employed. Initially, both responses were analyzed individually and then used to simultaneously maximize both variables. The optimized conditions of CTAB (500 mg/L), air flow of 2 L/min and volume of 600 mL resulted in a R of 91 % and CF of 19 times. Although a secondary step is necessary for further concentration, this technique utilizes 70 times less energy as compared to conventional centrifugation techniques which are used to recover Schizochytrium sp. This is significant as this technique can be easily adapted to existing bioreactors, as they are already equipped with gas spargers. In addition, the presence of surfactant carried through demonstrated an improvement in the recovery of long chain poly unsaturated fatty acid (PUFA) by 6 %, particularly in DHA and DPA which was not observed in washed biomass.