Naturally coloured cotton is environmentally friendly, since bleaching and chemical dyeing are not needed during textile production. Studying molecular-genetic mechanisms underpinning pigment production may facilitate breeding cotton with coloured fibre. In the current review we summarize the known data on structural and regulatory genes involved in biosynthesis of flavonoid pigments proanthocyanidins (PAs) in brown and caffeic acid (CA) in green fibre. The first chapter considers the first studies on fibre cotton inheritance, from the beginning of the last century. Then, we briefly review the biochemical and physico-chemical methods proving the presence of PAs in brown fibre and derivatives of CA in green cotton fibre. The biochemical analysis of coloured cotton fibre was followed by genetic studies of structural genes coding for enzymes participating in PA and CA biosynthesis, transport and oxidation processes. We summarize the data on the genes coding for transcription factors from the MBW (MYB-bHLH-WD40)