We study the zero mode solutions of a Dirac operator on a magnetized Riemann surface of higher genus. In this paper, we define a Riemann surface of higher genus as a quotient manifold of the Poincaré upper half-plane by a congruence subgroup, especially Γ 0 (N). We present a method to construct basis of cusp forms since the zero mode solutions should be cusp forms. To confirm our method, we select a congruence subgroup of semiprime level and show the demonstration to some lower weights. In addition, we discuss Yukawa couplings and matrix regularization as applications.