Microalgae have been increasingly used to generate biofuel, thus a sustainable technique should be implemented to harvest the biomass to ensure its existence in the environment. Aspergillus niger was used as bio-flocculant to harvest microalgae from aquaculture wastewater via flocculation technique over a range of pH and mixing rate. The bio-flocculant showed ability to adapt at a wide range of pH from 3.0 to 9.0 and at a mixing rate of 100-150 rpm, producing a harvesting efficiency of higher than 90%. The treated water possessed low concentration of chlorophyll-a (0.3-0.6 mg L-1) and cell density (2 × 106-3 × 106 cell mL-1). These indicate that Aspergillus niger is a promising bio-flocculant to be used in harvesting microalgae, thus promoting the use of flocculation as a green technology in aquaculture wastewater treatment.