To understand the fatigue mechanism of hot-dip galvanized steel, the fatigue strength and fracture surface of hot-dip galvanized S45C (carbon steel) specimens were investigated. The galvanized coating layer was composed of δ1-phase, ζ-phase and η-phase, and its thickness was about 100 μm. In low cycle range (104 cycles < Nf <105 cycles), the fatigue strengths of both the carbon steel and the galvanized steel corresponded to the static strength. The fatigue strength of the galvanized steel was lower than that of the carbon steel. As the number of cycles increased, the difference between fatigue strength of the carbon steel and that of the galvanized steel increased. In addition, the morphologies of the fatigue fracture were also different in low cycle range and high cycle range. In the galvanized steel, the morphology of stage II crack on the fracture surface at low cycle range exhibited crescent shape, and multiple crack initiation sites in low cycle range were observed. On the other hand, the morphology at high cycle region (Nf > 105 cycles) exhibited an ellipse shape, and the crack initiation site was single. At both ranges, the crack initiation sites were in the coating layer. The mechanical properties of the microstructure in coating layer affect on the fatigue strength. When η-phase was removed from the galvanized coating layer, the fatigue strength increased only in high cycle range. Therefore, δ1-phase and/or ζ-phase cause the fatigue strength to decrease in low cycle range, and η-phase causes it in high cycle range.