The isotropic harmonic oscillator in dimension 3 separates in several different coordinate systems. Separating in a particular coordinate system defines a system of three Poisson commuting integrals and, correspondingly, three commuting operators, one of which is the Hamiltonian. We show that the Lagrangian fibration defined by the Hamiltonian, the z component of the angular momentum, and a quartic integral obtained from separation in prolate spheroidal coordinates has a non-degenerate focus-focus point, and hence, non-trivial Hamiltonian monodromy for sufficiently large energies. The joint spectrum defined by the corresponding commuting quantum operators has non-trivial quantum monodromy implying that one cannot globally assign quantum numbers to the joint spectrum.