Single crystals of three soluble Yb@C(82) isomers, namely, Yb@C(2)(5)-C(82), Yb@C(s)(6)-C(82), and Yb@C(2v)(9)-C(82), cocrystallized with Ni(II)(octaethylporphyrin), allowed accurate crystallographic elucidation of their molecular structures in terms of both cage symmetry and metal location. Multiple metal positions were found in all these isomers, but the major metal sites were found in some specific regions within these cages. Specifically, the Yb(2+) ion prefers to reside close to a hexagonal ring in Yb@C(2)(5)-C(82) and Yb@C(2v)(9)-C(82) but a [5,6,6]-junction carbon atom in Yb@C(s)(6)-C(82). Theoretical calculations at the B3LYP level revealed that these metal positions all correspond to energy minima from the electrostatic potential maps and give rise to the most stable configurations of these Yb@C(82) isomers. Furthermore, it is noteworthy that this is the first report on X-ray crystallographic studies of such metallofullerenes with the popular C(2v)(9)-C(82) encapsulating a divalent metal ion, described as M(2+)@[C(2v)(9)-C(82)](2-).