The land around Marquette was known to French missionaries of the early 17th century and the trappers of the early 19th century. The area was originally and predominantly inhabited by the Noquet, Ojibwe, Odawa and Potawatomi, the latter three peoples comprising the Anishinaabe Council of Three Fires. They knew the area as Gichi-namebini-ziibing ("The river of giant white suckers", referring to the Dead River). Development of the area did not begin until 1844, when William Burt and Jacob Houghton (the brother of geologist Douglass Houghton) discovered iron deposits near Teal Lake west of Marquette. In 1845, Jackson Mining Company, the first organized mining company in the region, was formed.
The village of Marquette began on September 14, 1849, with the formation of a second iron concern, the Marquette Iron Company. Three men participated in organizing the firm: Robert J. Graveraet, who had prospected the region for ore; Edward Clark, agent for Waterman A. Fisher of Worcester, Massachusetts, who financed the company, and Amos Rogers Harlow. The village was at first called New Worcester, with Harlow as the first postmaster. On August 21, 1850, the name was changed to honor Jacques Marquette, the French Jesuit missionary who had explored the region. A second post office, named Carp River, was opened on October 13, 1851, by Peter White, who had gone there with Graveraet at age 18. Harlow closed his post office in August 1852. The Marquette Iron Company failed, while its successor, the Cleveland Iron Mining Company, flourished and had the village platted in 1854. The plat was recorded by Peter White. White's office was renamed as Marquette in April 1856, and the village was incorporated in 1859. It was incorporated as a city in 1871.
During the 1850s, Marquette was linked by rail to numerous mines and became the leading shipping center of the Upper Peninsula. The first ore pocket dock, designed by an early town leader, John Burt, was built by the Cleveland Iron Mining Company in 1859. By 1862, the city had a population of over 1,600 and a soaring economy.
In the late 19th century, during the height of iron mining, Marquette became nationally known as a summer haven. Visitors brought in by Great Lakes passenger steamships filled the city's hotels and resorts.