Magnetic nanocapsules were constructed by fabricating nanometer scaled C(60)-like "Keplerate" type {Mo(72)Fe(30)} with molecular formula [Mo(72)(VI)Fe(30)(III)O(252)(CH(3)COO)(12){Mo(2)O(7)(H(2)O)}(2){H(2)Mo(2)O(8)(H(2)O)}(H(2)O)(91)] x ca.150 H(2)O into nanocapsule shells using the LbL technique. The morphology of the obtained hybrid nanocapsules was examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Shell thickness of the {Mo(72)Fe(30)}-embedded nanocapsules can be tailored at the nanometer level more precisely than other nanoparticle-embedded capsules due to the homogeneous diameter and surface charges of {Mo(72)Fe(30)}. Interestingly, the {Mo(72)Fe(30)}-embedded nanocapsules could be separated and aligned under a circumstance of magnetic field, though {Mo(72)Fe(30)} is a paramagnetic molecule. This is the first time to fabricate hybrid magnetic materials containing {Mo(72)Fe(30)} using LbL technique. The obtained nanocapsules can be a good candidate for bioseparation as well as targeted delivery.