The red coleoptile in wheat confers antioxidant, photoprotective, and seedling stress-tolerance enhancing physiological functions. To provide key support for clarifying the molecular regulatory mechanism of the red coleoptile in wheat and improving the theory and technical system of morphological marker-assisted breeding, this study used a population of 127 F₁₂ recombinant inbred lines (RILs) derived from the cross between a common wheat Ning 7840 (white coleoptile, female parent) and Clark (red coleoptile, male parent) as materials. Quantitative trait loci (QTLs) controlling the red coleoptile were mapped using the inclusive composite interval mapping-additive effect (ICIM-ADD) method combined with a high-density genetic map containing 593 SNP and 402 SSR markers. Comparative genomics was used to align the collinear chromosomal regions between wheat and Brachypodium distachyon, sorghum, and rice to screen candidate genes related to anthocyanin regulation. Candidate genes were cloned, and sequence differences between red and white coleoptile lines were analyzed. CAPS markers were developed to verify gene-phenotype associations. The gene characteristics and functions were examined through subcellular localization and transient expression in wheat calli. The results showed that the ratio of red to white coleoptile lines in the RIL population conformed to 1∶1. A major QTL (qRc-7A) was detected on chromosome 7A, located between markers Xsnp7205 and Xsnp5258 (1.69 cM), explaining 66.4% of the phenotypic variation. Collinearity analysis revealed a collinear relationship between this mapped interval and the corresponding regions on chromosome 1 of Brachypodium distachyon, chromosome 10 of Sorghum bicolor, and chromosome 6 of Oryza sativa. Within the collinear regions of Sorghum bicolor and Oryza sativa, anthocyanin regulatory R2R3-MYB transcription factor-encoding genes, namely Sb10g06800 and Os06g10350 (OsC1), were identified, which shared high sequence similarity with the TraesCS7A02G165700 gene on wheat chromosome 7A. It was thus preliminarily inferred that TraesCS7A02G165700 is a key candidate gene regulating anthocyanin biosynthesis in the red coleoptile of wheat, and this gene was designated as TaC1. TaC1a in red coleoptile lines (cDNA length 774 bp, encoding 258 amino acids) contains a complete R2R3 domain and motif 5 domain, while TaC1b in white coleoptile lines has a frameshift mutation due to a 714 bp deletion, resulting in the loss of motif 5. TaC1a is localized in the nucleus and can induce anthocyanin accumulation in transient expression experiments in wheat calli, whereas TaC1b lacks this function. CAPS marker detection showed that TaC1a was significantly associated with the red trait, but 4 red coleoptile materials carried TaC1b. In conclusion, TaC1 is the core gene regulating anthocyanin synthesis in wheat red coleoptiles, and TaC1b loses its function due to base deletion. The CAPS marker based on this variation can be used for molecular identification of red coleoptite, but other regulatory genes may be involved in some red materials, requiring further analysis of multi-gene interaction mechanisms.