Berberine is a quaternary ammonium salt from the protoberberine group of isoquinoline alkaloids. It is found in such plants as Berberis (e.g. Berberis aquifolium (Oregon grape), Berberis vulgaris(Barberry), and Berberis aristata (Tree Turmeric)),Hydrastis canadensis (Goldenseal), Phellodendron amurense (Amur Cork Tree, Huang Bai, Huang Po, Po Mu) and Coptis chinensis (Chinese Goldthread, Huang-Lian, Huang-Lien), and Tinospora cordifolia, and to a smaller extent in Argemone mexicana (Prickly Poppy) and Eschscholzia californica (Californian Poppy). Berberine is usually found in the roots, rhizomes, stems, and bark.

Berberine is strongly yellow colored, which is why in earlier times Berberis species were used to dye wool, leather and wood. Wool is still today dyed with berberine in northern India. Under ultraviolet light, berberine shows a strong yellow fluorescence. Because of this it is used in histology for staining heparin in mast cells.As a natural dye, berberin has a Colour Index (CI) of 75160.