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In most animals, the brain controls the body via a set of descending neurons (DNs) that traverse the neck and terminate in post-cranial regions of the nervous system. This critical neural population is thought to activate, maintain and modulate locomotion and other behaviors. Although individual members of this cell class have been well-studied across species ranging from insects to primates, little is known about the overall connectivity pattern of DNs as a population. We undertook a systematic anatomical investigation of descending neurons in the fruit fly, Drosophila melanogaster, and created a collection of over 100 transgenic lines targeting individual cell types. Our methods allowed us to describe the morphology of roughly half of an estimated 400 DNs and create a comprehensive map of connectivity between the sensory neuropils in the brain and the motor neuropils in the ventral nerve cord. Like the vertebrate spinal cord, our results show that the fly nerve cord is a highly organized, layered system of neuropils, an organization that reflects the fact that insects are capable of two largely independent means of locomotion -- walking and fight -- using distinct sets of appendages. Our results reveal the basic functional map of descending pathways in flies and provide tools for systematic interrogation of sensory-motor circuits.