When one element in an apparent motion sequence differs in color from the others, it is perceived as shifted along the motion trajectory. We examined whether V4 neurons encode the physical or perceived location of this "flashed" element by recording neuronal responses while monkeys viewed these stimuli. The retinotopic locus of V4 activity evoked by the flashed element shifted along the motion trajectory. The magnitude of the shift is consistent with the perceptual shift in humans viewing identical stimuli. This retinotopic distortion depended on the presence of a flashed element but was observed for both color-selective and non-color-selective neurons. The distortion was undiminished when the flashed element terminated the sequence, a condition that reduced the perceptual shift in humans. These findings are consistent with a Bayesian model of localization in which perceived location is derived from position signals optimally integrated across visual areas.