Market available fermented indigo powders of Indian origin (FI1, FI2), Chinese origin (FC1, FC2), and raw indigo powders of Indian origin (R1, R2) were examined using TLC and HPLC analyses to investigate their pigment contents. TLC analysis gave Rf values of 0.81 and 0.72 for blue and red pigments, respectively. All the powder products and the synthetic and natural indigo standards eluted at 6.9 min and 8.3 min in the HPLC chromatograms, and the peaks showed the λmax at 610nm and 542nm, representing indigotin and indirubin, respectively. The pigment content calculated based on the area of indigotin and indirubin peaks in the HPLC chromatograms showed that the indigotin content was higher in FC1 and FC2, while FI1 and FI2 had a higher indirubin content. The relative percentage of indirubin was the highest in R2, but the HPLC peak intensity was quite low. Despite the higher indigotin content in FC1 and FC2, cotton dyed with FI1 and FI2 (versus cotton dyed with FC1 and FC2) showed a higher blue (B) hue, the highest K/S values, and the highest antimicrobial effect.