This study examined the dosimetric influence of implanted gold markers in proton therapy and the effects of their positions in the spread-out Bragg peak (SOBP) proton beam. The implanted cylindrical gold markers were 3 mm long and 1.2 mm in diameter. The dosimetric influence of the gold markers was determined with markers at various locations in a proton-beam field. Spatial dose distributions were measured using a three-dimensional moving water phantom and a stereotactic diode detector with an effective diameter of 0.5 mm. Also, a film dosimetry was performed using Gafchromic External Beam Treatment (EBT) film. The GEANT4 simulation toolkit was used for Monte-Carlo simulations to confirm the measurements and to construct the dose-volume histogram with implanting markers. Motion data were obtained from the portal images of 10 patients to investigate the effect of organ motions on the dosimetric influence of markers in the presence of a rectal balloon. The underdosed volume due to a single gold marker, in which the dose was less than 95% of a prescribed amount, was 0.15 cc. The underdosed volume due to the presence of a gold marker is much smaller than the target volume. However, the underdosed volume is inside the gross tumor volume and is not smeared out due to translational prostate motions. The positions of gold markers and the conditions of the proton-beam field give different impacts on the dose distribution of a target with implanted gold markers, and should be considered in all clinical proton-based therapies.