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ABSTRACTAmaranth is rich in betalain. Both betalain metabolites and plant growth are affected by external factors. However, studies of amaranth seedling growth and betalain metabolism are limited by a lack of appropriate reference genes for qRT-PCR analyses. We selected 13 candidate reference genes from the amaranth transcriptome database and tested their expression stability under various environmental conditions and plant growth regulators. Five methods were used for the analysis: geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder. The most stable reference genes were SANDand RAN1for light quality, SANDand EIF5afor photoperiod, Actin-7and TuAfor temperature, SANDand Actin-7for different tissue, SANDand EIF5afor NaCl, SANDand 60S RPLfor GA3, 28S rRNAand 18S rRNAfor 6-BA, 18S rRNAand 60S RPLfor 2,4-D, EIF5aand 28S rRNAfor ABA, Actin-11and SKIP35for SA, 28S rRNAand Actin-7for MeJA, SANDand EIF5afor all samples. To further verify the reliability of the reference genes identified in this study, the expression levels of CYP76AD1were studied in amaranth. This is the first systematic analysis aimed at the selection of reference genes for qRT-PCR in A. tricolorunder different culture conditions.