In this paper, we investigate the "Hamiltonian'' monodromy of the fibration in Liouville tori of certain integrable systems via (real) algebraic geometry. Using Picard-Lefschetz theory in a relative Prym variety, we determine the Hamiltonian monodromy of the "geodesic flow on $SO(4)$''. Using a relative generalized Jacobian, we prove that the Hamiltonian monodromy of the spherical pendulum can also be obtained by Picard-Lefschetz formula.