Zinc is an essential element, which is toxic for organisms in their natural environments in excessive amounts. The zinc accumulation characteristics of a Zn-tolerant strain (H93, EC₅₀ = 1010 mg·L^–1 Zn²⁺) and a Zn-sensitive strain (B40-3, EC₅₀ = 26 mg·L^–1 Zn²⁺), Exophiala spp. and their antioxidant response to Zn²⁺ stress were comparatively characterized. Under their respective Zn²⁺ median effective concentrations, H93 absorbed 2.5-fold and accumulated 5.2-fold more Zn than B40-3. An elution experiment using CaCl₂ revealed that Zn mainly accumulated intracellularly in the mycelia of the two fungal strains. The modulation of antioxidant components and antioxidant enzyme activities of the two fungal strains were comparatively analyzed under different Zn²⁺ concentrations. The activity of the total superoxide dismutase, peroxidase, and glutathione of H93 was always higher than that of B40-3, and the malondialdehyde content in H93 was also higher than that of B40-3. The current results suggested that the Zn tolerance of Exophiala strain may be attributed to their various instinctive behaviors with different rates of Zn accumulation and modulation of antioxidant components.