Natural Indigo, primarily from Indigofera tinctoria or Baphicacanthus cusia, perhaps most famously known these days for dying denim jeans.
Several species of plant bear indigo, so it is not totally clear whether Colour Index designation only applies to the traditional Indigofera tinctoria or if it applies to other species or methods of creating indigotin, such as the weaker blue-bearing Woad, (Satis tinctoria).
Sasha Duerr's Natural Palettes discusses a different indigo species which is a bit easier to grow in cooler climates, Persicaria tinctoria or Japanese Indigo leaves.
In terms of painting, CAMEO notes that it may be added directly to binding media. "Indigo is a fine, intense powder which may be used directly as a pigment in oil, tempera, or watercolor media. The exposed pigment can fade rapidly in strong sunlight." This is thought to be fugitive (about ASTM III).
We were saddened and surprised to learn that natural indigo can actually be quite toxic. See Monona Rossol's research for more.
