Differential flocculation acts based upon the difference in the settling rates of two minerals. So, the application of the bacterial cells, spent medium, extracellular protein, and polysaccharide derived from a cell-free extract of Bacillus licheniformis were investigated to remove hematite and goethite from kaolin and quartz. The zeta potentials and settling behaviors of the minerals in the presence and absence of the bioflocculants at various pH values were explored. The adsorption density of each bioflocculant on the minerals was measured and compared relatively, for various pH settings, while the adsorption isotherm of each bioreagent was determined at the neutral pH, as well. Polysaccharide presented the best settling differences at pH 7 that were 66.7%, 58.4%, 53.7%, and 45.4% for the hematite-quartz, goethite-quartz, hematite-kaolin, and goethite-kaolin pairs, respectively. It showed the best ability for the removal of iron oxides at pH 7 (approximate to 76%-84%) with almost 56%-69% separation efficiency, respectively.