In 1872 he published his "Key to North American Birds", which, revised and rewritten in 1884 and 1901, did much to promote the systematic study of ornithology in America. He was a founding member of the American Ornithologists' Union in 1883. His work was instrumental in establishing the currently accepted standards of trinomial nomenclature – the taxonomic classification of subspecies – in ornithology, and ultimately the whole of zoology. During 1873–1876 Coues was attached as surgeon and naturalist to the United States Northern Boundary Commission, and from 1876 to 1880 he was secretary and naturalist to the United States Geological and Geographical Survey of the Territories, the publications of which he edited. He was lecturer on anatomy in the medical school of the Columbian University from 1877 to 1882, and professor of anatomy there from 1882 to 1887.