Although a high risk of contamination is associated with ambient bacteria during fermentation, the fermentation fluid maintains a reduced state for up to 6 months on average. However, the mechanisms underlying the occurrence of indigo reduction in a short period and the maintenance of reduced state in the indigo fermentation fluid by the microbiota over such a long period remain unclear. We study on the changes of microbiota during occurrence of indigo reduction at the initiation of the fermentation. We also study on microbiota on long-lasting (longer than 6 months) indigo fermentation fluids. In addition, we attempted to identify the characteristics and dynamics of the microbiota in the initiation of indigo reduction and the long-lasting indigo fermentation fluids in a reduced state under natural fermentation conditions in the open air.