Unique properties of biogenic Mn oxides were applied to a fundamental study of separation and recovery of rare earth elements. Selective sorption of Ce3+ over La3+ ions was achieved at neutral pH values using biogenic Mn oxides produced by Paraconiothyrium sp. WL-2 strain. The selective coefficient for Ce3+ (αCe) was much greater with biogenic and synthetic Mn oxides than those for La3+ (αLa). Ce3+ ions were oxidized to CeO2 by Mn(III, IV) in Mn oxides under anaerobic conditions resulting in the release of Mn2+ ions, while La3+ ions were sorbed without a redox reaction. With an increase in coexisting La3+ ions, sorption of Ce3+ on both Mn oxides was significantly suppressed, especially with synthetic Mn oxides. The edges of the structure are competitive sites because of fewer numbers of vacant sites in synthetic Mn oxide layers. The preferential sorption on the edge sites of Mn oxides is in the order of La3+ > Ce3+. These phenomena can be expanded to separation and recovery of other rare earth elements from natural and anthropogenic sources.