The brainstem consists of the entire caudal region of the brain beneath the cerebellum, behind the thalamus, and in front of the spinal cord. It is the huge stalk of the brain which contains all the sensory, motor and interconnecting cellular groups, together with all the fiber tracts which pass through this region. The fiber tracts that interconnect the forebrain (thalamus, basal forebrain, and cerebral cortex), spinal cord, and cerebellum.

This region of the brain is depicted below in the coronal sections of one manatee, #85-32, which extends from the caudal part of the thalamus down to the rostral portion of the spinal cord (that is, the first cervical spinal segment within the vertebrae of the upper neck.