To analyse the functioning of the amygdala in depression, we performed the first voxel-level resting state functional-connectivity neuroimaging analysis of depression of voxels in the amygdala with all other voxels in the brain, with 336 patients with major depressive disorder and 350 controls. Amygdala voxels had decreased functional connectivity (FC) with the orbitofrontal cortex, temporal lobe areas, including the temporal pole, inferior temporal gyrus and the parahippocampal gyrus. The reductions in the strengths of the FC of the amygdala voxels with the medial orbitofrontal cortex and temporal lobe voxels were correlated with increases in the Beck Depression Inventory score and in the duration of illness measures of depression. Parcellation analysis in 350 healthy controls based on voxel-level FC showed that the basal division of the amygdala has high FC with medial orbitofrontal cortex areas, and the dorsolateral amygdala has strong FC with the lateral orbitofrontal cortex and related ventral parts of the inferior frontal gyrus. In depression, the basal amygdala division had especially reduced FC with the medial orbitofrontal cortex, which is involved in reward; and the dorsolateral amygdala subdivision had relatively reduced FC with the lateral orbitofrontal cortex, which is involved in non-reward.