We study the modular invariance in magnetized torus models. Modular invariant flavor model is a recently proposed hypothesis for solving the flavor puzzle, where the flavor symmetry originates from modular invariance. In this framework coupling constants such as Yukawa couplings are also transformed under the flavor symmetry. We show that the low-energy effective theory of magnetized torus models is invariant under a specific subgroup of the modular group. Since Yukawa couplings as well as chiral zero modes transform under the modular group, the above modular subgroup (referred to as modular flavor symmetry) provides a new type of modular invariant flavor models with $D_4 \times _2(_4 \times _2) \rtimes _2(_8 \times _2) \rtimes _2$. We also find that conventional discrete flavor symmetries which arise in magnetized torus model are non-commutative with the modular flavor symmetry. Combining both two symmetries we obtain a larger flavor symmetry, where the conventional flavor symmetry is a normal subgroup of the whole group.

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