Abstract:[Background] Indigoidine is a nontoxic blue pigment produced by microorganisms. [Objective] Comparison of the stability of heterologous expressed indigoidine in Escherichia coli and commercial indigo. [Methods] Recombinant E. coli DH5α/p28s strain was constructed to produce indigoidine. The effects of light, UV, pH, temperature, oxidant, reductant, food additive, metal ion on the stability of the two pigments were investigated. [Results] When N,N-dimethylformamide (DMF) was used as solvent, both indigoidine and indigo were sensitive to visible light and UV. The colors of the two pigments were stable at pH 1.0?11.0, but higher pH had a great destructive effect. The tolerance of indigoidine to Vc reduction was stronger than that of indigo. Both maximal absorption values were reduced at a certain degree by oxidant. Indigoidine showed distinguished better thermal stability than indigo below 75 °C, but both were bleached at higher temperature. The food additive citric acid and benzoic acid had significant protective effect on the stability of indigoidine and indigo respectively. Ca2+ and Mg2+ showed certain color-keeping effect on both pigments, while Na+, K+ and Li+ had no overall destruction impact, but Zn2+, Al3+, Cu2+, Fe2+ and Fe3+ exhibited notable destruction on both. [Conclusion] Indigoidine exhibits much better overall stability than indigo, suggesting a broader prospect of development and application.