The harvesting of microalgae is currently one of the bottlenecks hindering the commercial production of microalgae-based biofuels and products. The objective of this study was to determine the best flocculant and its optimum concentration in order to harvest the marine microalga Conticribra weissflogii (previously Thalassiosira weissflogii) for further use in the production of biofuels or bioelements. Experiments were conducted with cultures in the logarithmic and stationary growth phases. The low-charge FLOPAM® FO 4240 SH was the most effective at concentrations of 2 and 4 mg m−3 in the LOG phase cultures, with flocculation efficiencies >90%. Smaller flocculation efficiencies were observed for cells in the stationary growth phase, most likely due to the production of dissolved organic carbon by the microalga. The highest microalgae density generated higher flocculation rates, whereas the pH and salinity negatively impacted flocculant efficiency.