We employed high-resolution fMRI to distinguish the impacts of anisometropia and strabismus amblyopia on the evoked ocular dominance (OD) response. Sixteen amblyopic participants (eight females) plus eight individuals with normal vision (one female), participated in this study for whom we measured the difference between the response to stimulation of the two eyes, across areas V1–V4. In controls, the evoked OD response formed the expected striped pattern within V1. Compared to controls, the OD response in amblyopic participants formed larger fused patches that extended into downstream visual areas. Moreover, both anisometropic and strabismic participants showed elevated OD responses across V1–V4. Beyond these common effects, and despite similar densities of amblyopia between the two groups, strabismus, and anisometropia had differential impacts on the OD bias, binocular response, and correlation between V1 depth levels. Specifically, we found a greater increase in the size of the V1 portion that responded preferentially to fellow eye stimulation in anisometropic compared with strabismic individuals. We also found a greater difference between the amplitudes of the response to binocular stimulation, in those regions that responded preferentially to the fellow versus amblyopic eye, in anisometropic compared with strabismic participants. In contrast, strabismic participants demonstrated an increased correlation between the OD responses evoked within V1 superficial and deep depths, whereas anisometropic individuals did not. These results provide the primary direct functional evidence for distinct impacts of strabismus and anisometropia on the mesoscale functional organization of the human visual system, thus extending what was inferred previously about amblyopia from animal models.