Magnetic flocculant was synthesized for the highly efficient recovery of microalgal cells. The highest flocculation was achieved using the magnetic flocculant synthesized with iron oxide and 0.1 mg/mL cationic polyacrylamide (CPAM). This resulted in a recovery efficiency of more than 95% within 10 min using a dosage of 25 mg/L for Botryococcus braunii and 120 mg/L for Chlorella ellipsoidea. For both species, the adsorption isotherm data fit the Freundlich model better than the Langmuir model, indicating that the adsorption process was a heterogeneous multilayer. The maximum adsorption capacity was 114.8 and 21.4 mg dry cells/mg-particles at pH 7 for B. braunii and C. ellipsoidea, respectively. The primary flocculation mechanism was bridging, which was assisted by the electrostatic interactions between the microalgal cells and the magnetic flocculant under acidic conditions. These results provide new opportunities and challenges for understanding and improving the harvesting of microalgae using magnetic separation.