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In magnetized plasmas of fusion devices the strong magnetic field leads to highly anisotropic physics where solution scales along field lines are much larger than perpendicular to it. Hence, regarding both accuracy and efficiency, a numerical method should allow to address parallel and perpendicular resolutions independently. In this work, we consider the eigenvalue problem of a two-dimensional anisotropic wave equation with variable coefficients which is a simplified model of linearized ideal magnetohydrodynamics. For this, we propose to use a mesh that is aligned with the magnetic field and choose to discretize the problem with a discontinuous Galerkin method which naturally allows for non-conforming interfaces. First, we analyze the eigenvalue spectrum of a constant coefficient anisotropic wave equation, and demonstrate that this approach improves the accuracy by up to seven orders of magnitude, if compared to a non-aligned method with the same number of degrees of freedom. In particular, the results improve for eigenfunctions with high mode numbers. We also apply the method to compute the eigenvalue spectrum of the associated anisotropic wave equation with variable coefficients of flux surfaces of a Stellarator configuration. We benchmark the results against a spectral code.