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We study a geometric transition in non-perturbative topological string. We consider two cases. One is the geometric transition from the closed topological string on the local to the closed topological string on the resolved conifold. The other is the geometric transition from the closed topological string on the local to the open topological string on the resolved conifold with a toric A-brane. We find that, in both cases, the geometric transition can be applied for the non-perturbative topological string. We also find the corrections of the value of K"ahler parameters at which the geometric transition occurs.

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