The stability properties of the Hill equation are discussed, especially those of the Mathieu equation that characterize ion motion in electrodynamic traps. The solutions of the Mathieu-Hill equation for a trapped ion are characterized by employing the Floquet theory and Hill’s method solution, which yields an infinite system of linear and homogeneous equations whose coefficients are recursively determined. Stability is discussed for parameters a and q that are real. Characteristic curves are introduced naturally by the Sturm–Liouville problem for the well-known even and odd Mathieu equations cem(z,q) and sem(z,q). In the case of a Paul trap, the stable solution corresponds to a superposition of harmonic motions. The maximum amplitude of stable oscillations for ideal conditions (taken into consideration) is derived. We illustrate the stability diagram for a combined (Paul and Penning) trap and represent the frontiers of the stability domains for both axial and radial motion, where the former is described by the canonical Mathieu equation. Anharmonic corrections for nonlinear Paul traps are discussed within the frame of perturbation theory, while the frontiers of the modified stability domains are determined as a function of the chosen perturbation parameter and we demonstrate they are shifted towards negative values of the a parameter. The applications of the results include but are not restricted to 2D and 3D ion traps used for different applications such as mass spectrometry (including nanoparticles), high resolution atomic spectroscopy and quantum engineering applications, among which we mention optical atomic clocks and quantum frequency metrology.