DNA-immobilized Fe3O4 particles (DNA–Fe-particles) were prepared by mixing DNA, magnetic Fe3O4 particles, and the silane coupling reagent, bis[3-(trimethoxysilyl)propyl]amine. The DNA–inorganic hybrid material was uniformly immobilized onto magnetic Fe3O4 particles with the diameters of approximately 450 nm. These DNA–Fe-particles were stable in water. Additionally, we could simply collect the DNA–Fe-particles by a magnet from an aqueous solution. Therefore, we demonstrated the accumulation of various metal ions, such as heavy and rare-earth metal ions, by the DNA–Fe-particles. As a result, although these DNA–Fe-particles could selectively accumulate heavy and rare-earth metal ions, these materials could not accumulate the light metal ions, such as Mg(II) and Ca(II) ions. Furthermore, the metal ion-accumulated DNA–Fe-particles could be recycled by washing them with an aqueous ethylenediaminetetraacetic acid solution.