Limb amputation results in plasticity of connections between the brain and muscles; the cortical motor representation of the missing limb seemingly disappears. The disappearance of the hand's motor representation is, however, difficult to reconcile with evidence that a perceptual representation of the missing limb persists in the form of a phantom limb endowed with sensory and motor qualities. Here, we argue that despite considerable reorganization within the motor cortex of upper-limb amputees, the representation of the amputated hand does not disappear. We hypothesize that two levels of hand-movement representation coexist within the primary motor cortex; at one level, limb movements are specified in terms of arm and hand motor commands, and at another level, limb movements are specified as muscles synergies. We propose that primary motor cortex reorganization after amputation concerns primarily the upper limb's muscular map but not its motor command map and that the integrity of the motor command map underlies the existence of the phantom limb.