Background: The appearance of synthetic indigo has caused most people to forget the past brilliance of natural indigo. However, in parts of southern China, the folk still use and trade in natural indigo paste. The aims of this study were to i) document the traditional knowledge and experience of how people identify the quality of indigo paste and ii) explore the rationality of the quality judgment index used by local people.Method: We interviewed 283 traditional indigo paste artisans in 3 markets and 15 villages in Guizhou, Yunnan, and Fujian Provinces. Frequency of citation (FC), Mention index (QI), and Fidelity level (FL) of each indigo paste quality judgment index were calculated to determine the most commonly used, most recognized, and most important quality judgment index. A quantitative study was conducted on 21 indigo paste samples of different quality grades using high-performance liquid chromatography with diode-array detection (HPLC-DAD), an acidity meter, and particle size analyzer. The relationship between the content of the effective components, pH, and particle size of the indigo paste and quality was explored. Results: The people divided indigo paste into five quality grades i.e., best, good, general, poor, and worst. Four main quality judgment indices were color, taste, touch, and dyeing ability. Among all study areas, color was the most commonly used, most important, and most recognized index. Effective ingredient content and pH differed significantly with different quality graded indigo pastes, but there was no significance difference between particle size and quality. In addition to indigo, indirubin played an important role in identifying the quality of indigo paste.Conclusion: Our study confirmed that the quality of indigo paste could be evaluated using the four indices (color, taste, touch, and dyeing ability). The people used indigo and indirubin content together to determine the quality of the indigo paste, while synthetic indigo is determined by indigo content only. The simple knowledge and experience of traditional folk has guiding significance for the modern development of indigo paste production.