We study the modular symmetry of zero-modes on {T}_1^2times {T}_2^2 and orbifold compactifications with magnetic fluxes, M1, M2, where modulus parameters are identified. This identification breaks the modular symmetry of {T}_1^2times {T}_2^2 , SL(2, ℤ)1× SL(2, ℤ)2 to SL(2, ℤ) ≡ Γ. Each of the wavefunctions on {T}_1^2times {T}_2^2 and orbifolds behaves as the modular forms of weight 1 for the principal congruence subgroup Γ(N), N being 2 times the least common multiple of M1 and M2. Then, zero-modes transform each other under the modular symmetry as multiplets of double covering groups of ΓN such as the double cover of S4.
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