This is the first study on production of three dimensional chitinous microcages from ephippial eggs of a microcrustacean, Daphnia longispina (water flea) by keeping the original shape of its chitinous structure. Iron-based magnetic particles were successfully loaded into the chitinous microcages to enhance its heavy metal sorption capacity. The FT-IR, SEM-EDX and TGA analysis proved the purity of chitin and demonstrated that the loading of magnetic particles into the chitinous microcages was achieved. These newly obtained three-dimensional chitin microcages and magnetic particles loaded microcages were tested in Cd(II), Cr(III), Cu(II), Ni(II) and Zn(II) removal from aqueous solutions. Magnetic particles loaded microcages exhibited a better performance in removal of Cd(II), Cu(II) and Ni(II) ions; while unloaded microcages showed a higher affinity for Cr(III) and Zn(II). This study demonstrated that the chitin microcages are suitable carriers for iron-based magnetic particles. Here these new materials were studied only for removal of five heavy metal ions but these promising materials have a potential to be used in various fields.