Natural · Antiquity to the late 19th century (before synthetic indigo)

Indigo dye is one of the oldest known dyes, traded across multiple continents for millennia before synthetic indigo production began in the late 19th century.
Indigo-dyed fibre varies considerably by dye strength, number of dips and how the yarn has aged — this is one specific dyed sample, not a definitive indigo shade.Photo: “Indigo Dyed Yarn” by Loggie-log, Public domain, via Wikimedia Commons.
Indigo is a small organic molecule, indigotin, in which two ring systems are joined by a carbon–carbon double bond flanked by carbonyl and amine groups. That compact, cross-conjugated arrangement, stiffened by internal hydrogen bonds, absorbs orange-red light and so looks deep blue. Indigotin is insoluble in water; it becomes soluble only when chemically reduced to a pale 'leuco' form, which oxidises back to blue in air — the basis of vat dyeing.
The leaves of indigo-bearing plants — Indigofera species in the tropics, woad in Europe — contain a colourless precursor, indican. Soaking the leaves let it break down; the liquor was then beaten or aerated so the blue formed and settled, and the sludge was dried into cakes for trade. Dyers dissolved it again in fermentation vats, historically often based on stale urine. Indigo was a major colonial crop in India, the Americas and West Africa, with a history of forced labour behind much of that trade.
On cloth, indigo is the most lightfast of the natural organic dyes, and its familiar fading on denim is mostly mechanical: the dye sits near the fibre surface, so abrasion wears it away to reveal the white core. As a paint pigment it behaves worse. Finely dispersed in oil or glue, it is vulnerable to light, and blues in some 17th- and 18th-century paintings have faded or greyed; painters largely abandoned it in oil by the early 18th century. Analysis of a faded blue dress in an American colonial portrait found indigo mixed with Prussian blue.
Being organic, indigo is invisible to XRF, so conservators rely on molecular methods. Raman spectroscopy and surface-enhanced Raman (SERS) identify indigotin even in tiny, faded samples; reflectance spectroscopy shows its characteristic absorption; and on textiles, extraction followed by liquid chromatography separates indigotin from related compounds such as indirubin. The same methods cannot say whether a sample is plant or synthetic indigo without trace markers.
Adolf von Baeyer synthesised indigo in 1878–80, and BASF began commercial production in 1897; within two decades the plant trade had collapsed. Synthetic indigo is the identical molecule, purer and consistent, and it dyes nearly all blue denim. In paint, where indigo was always fragile, it was replaced by Prussian blue, synthetic ultramarine and, later, phthalocyanine blue, with 'indigo' paint colours today usually being mixtures of these.
FactModerate evidence
Indigo is formed when the plant glucoside indican is split and the released indoxyl oxidises in air; it is the most lightfast of the natural organic dyes.
Source: Indigo — ColourLex pigment page
FactModerate evidence
Indigo is insoluble in water; vat dyeing reduces it to soluble leuco-indigo, which reverts to the insoluble blue when the cloth meets air.
Source: Indigo dye — Wikipedia
FactStrong evidence
SERS analysis of an apparently faded blue dress in a colonial American portrait found indigo mixed with the cheaper Prussian blue.
Caveat: One painting; it shows the mixture existed, not how common it was.
FactModerate evidence
Baeyer synthesised indigo between 1878 and 1880, and BASF brought synthetic indigo to market in 1897, after which natural production fell sharply.
Source: Indigo dye — Wikipedia; Indigo — ColourLex pigment page