Isaac Newton introduced Indigo as one of the seven base colors of his work. In the mid-1660s, when Newton bought a pair of prisms at a fair near Cambridge, the East India Company had begun importing Indigo dye into England, supplanting the homegrown woad as source of blue dye. In a pivotal experiment in the history of optics, the young Newton shone a narrow beam of sunlight through a prism to produce a rainbow-like band of colors on the wall. In describing this optical spectrum, Newton acknowledged that the spectrum had a continuum of colors, but named seven: "The originall or primary colours are Red, yellow, Green, Blew, & a violet purple; together with Orang, Indico, & an indefinite varietie of intermediate gradations." He linked the seven prismatic colors to the seven notes of a western major scale, as shown in his color wheel, with orange and Indigo as the semitones. Having decided upon seven colors, he asked a friend to repeatedly divide up the spectrum that was projected from the prism onto the wall:

The French Army adopted dark blue Indigo at the time of the French Revolution, as a replacement for the white uniforms previously worn by the Royal infantry regiments. In 1806, Napoleon decided to restore the white coats because of shortages of Indigo dye imposed by the British continental blockade. However, the greater practicability of the blue color led to its retention, and Indigo remained the dominant color of French military coats until 1914.

Light Indigo (web color indigo) represents the way the color Indigo was always reproduced in pigments, paints, or colored pencils in the 1950s. By the 1970s, because of the advent of psychedelic art, artists became used to brighter pigments, and pigments called "bright indigo" or "bright blue-violet" that are the pigment equivalent of the electric Indigo reproduced in the section above became available in artists' pigments and colored pencils.

Marina Warner's novel Indigo (1992) is a retelling of Shakespeare's The Tempest and features the production of Indigo dye by Sycorax.

'Tropical Indigo' is the color that is called añil in the Guía de coloraciones (Guide to colorations) by Rosa Gallego and Juan Carlos Sanz, a color dictionary published in 2005 that is widely popular in the Hispanophone realm.

Like many other colors (orange, rose, and violet are the best-known), Indigo gets its name from an object in the natural world—the plant named Indigo once used for dyeing cloth (see also Indigo dye).

However, it wasn’t until 1640 when demand started to pick up for Indigo. Spanish explorers discovered an American species of Indigo and began to cultivate the product in Guatemala. The English and French subsequently began to encourage Indigo cultivation in their colonies in the West Indies.