Coues (pronounced Cows) was born in Portsmouth, New Hampshire. He graduated at Columbian University, (now, George Washington University) Washington, D.C., in 1861, and at the Medical school of that institution in 1863. He served as a medical cadet in Washington in 1862-1863, an in 1864 was appointed assistant-surgeon in the regular army. 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. 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. In 1873-1876 Coues was attached as surgeon and naturalist to the United States Northern Boundary Commission, and in 1876-1880 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 in 1877-1882, and professor of anatomy there in 1882-1887.
He was a careful bibliographer and in his work on the Birds of the Colorado Valley he included a special section on swallows and attempted to resolve whether they migrated in winter or hibernated under lakes as was believed at the time:
He resigned from the army in 1881 to devote himself entirely to scientific research. He was a founder of the American Ornithologists' Union, and edited its organ, The Auk, and several other ornithological periodicals. He died in Baltimore, Maryland.
In addition to ornithology he did valuable work in mammalogy; his book Fur-Bearing Animals (1877) being distinguished by the accuracy and completeness of its description of species, several of which were already becoming rare.
He took an interest in spiritualism and began speculations in theosophy. He felt the inadequacy of formal orthodox science in dealing with the deeper problems of human life and destiny. Convinced by the principles of evolution, he believed that these principles may be capable of being applied in psychic research and he proposed to use it to explain obscure phenomena such as hypnotism, clairvoyance, telepathy and the like. For this he visited Madame Blavatsky in Europe. He then founded the Gnostic Theosophical Society of Washington, and in 1890 he became the president of the Esoteric Theosophical Society of America. Around this time he also exposed Blavatsky and lost his interest in the theosophical movement.
Among the most important of his publications, in several of which he had collaboration, are A Field Ornithology (1874); Birds of the North-west (1874); Monographs on North American Rodentia, with J. A. Allen (1877); Birds of the Colorado Valley (1878); A Bibliography of Ornithology (1878-1880, incomplete); New England Bird Life (1881); A Dictionary and Check List of North American Birds (1882); Biogen, A Speculation on the Origin and Motive of Life (1884); The Daemon of Darwin (1884); Can Matter Think? (1886); and Neuro-Myology (1887). He also contributed numerous articles to the Century Dictionary, wrote for various encyclopaedias, and edited the Journals of Lewis and Clark (1893), The Travels of Zebulon M. Pike (1895) and "the personal narrative of Charles Larpenteur", Forty Years a Fur Trader on the Upper Missouri (1833-1872), published in 1898.