  We study chiral zero-mode wave functions on blow-up manifolds of $T^2/Z_N$
orbifolds with both bulk and localized magnetic flux backgrounds. We introduce
a singular gauge transformation in order to remove $Z_N$ phases for $Z_N$
twisted boundary condition of matter fields. We compute wave functions of not
only bulk zero modes but also localized modes at the orbifold singular points,
which correspond to new zero modes induced by localized flux. By studying their
Yukawa couplings, it turns out that only three patterns of Yukawa couplings are
allowed. Our theory has a specific coupling selection rule.
