He was born at Salins, in the département of Jura, in France. He was educated at Besançon and at the Collège Saint Louis, Paris. After completing his studies, he made several excursions through Switzerland to recover his health. These trips led him to devote himself to natural science. During these trips, he met Jules Thurmann (1804-1855), who in turn introduced him to Louis Agassiz.
In 1845, he worked with Thurmann on a geological survey of the Jura mountains. He was appointed assistant in the mineralogical department of the Sorbonne in 1846, and also classified its collection of fossils. During this time, he conducted geological investigations in various parts of Europe. In 1847 he went to North America as traveling geologist for the Jardin des Plantes, charged with studying the United States and the English possessions in North America. In the following year, he joined Agassiz in Boston, and accompanied him to the Lake Superior region, visiting the copper mines of the Keweenaw Peninsula, Lake Huron, and Niagara. After six months, he returned to Cambridge, Massachusetts, and sent minerals he had collected to Paris.
In January 1849, Marcou directed his attention to the geology of New Jersey, Pennsylvania, and Virginia. Later he crossed the Allegheny Mountains, visiting the Mammoth Cave and other localities, and then traversed Canada. He returned to Europe for a short time in 1850. In 1853 he published a Geological Map of the United States, and the British Provinces of North America. In 1853 he entered the service of the United States government, and was the first geologist that crossed the United States, being attached to the Pacific Railroad Survey along the 35th parallel. one of a series of explorations of the American West to find possible routes for a transcontinental railroad. He subsequently made a geological section extending from the Mississippi River to the Pacific Ocean.
In 1855 he became professor of geology and palaeontology at the polytechnic school of Zürich, but relinquished this office in 1859, and in 1861 again returned to the United States, when he assisted Louis Agassiz in founding the Museum of Comparative Zoology, and was in charge of its palaeontological division from 1860 to 1864. Subsequently he devoted himself to scientific research until 1875, when he again entered the service of the United States government, and accompanied the Wheeler Survey to Southern California.
- Life, letters, and works of Louis Agassiz (1895)
- Cretaceous formations of the Jura
- Dyas (Permian) of Nebraska
- Taconic rocks of Vermont and Canada
- American Geological Classification and Nomenclature (1888)
- Geological Map of the World (1861, 2nd ed. 1875)
- A Little More Light on the United States Geological Survey (1892)
- Lettres sur les roches du Jura et leur distribution géographique dans les deux hémisphères (1857-1860)
- Geology of North America (1858)
- Gilman, D. C.; Thurston, H. T.; Colby, F. M., eds. (1905). "Marcou, Jules". New International Encyclopedia (1st ed.). New York: Dodd, Mead.
- One or more of the preceding sentences incorporates text from a publication now in the public domain: Chisholm, Hugh, ed. (1911). "Marcou, Jules". Encyclopædia Britannica (11th ed.). Cambridge University Press.
- Rines, George Edwin, ed. (1920). "Marcou, Jules". Encyclopedia Americana.
- Wilson, James Grant; Fiske, John, eds. (1900). "Marcou, Jules". Appletons' Cyclopædia of American Biography. New York: D. Appleton.
- Hubert Lyman Clark (1933). "Marcou, Jules". Dictionary of American Biography. New York: Charles Scribner's Sons.