The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs (chromosome 1B) and (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was , encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified and , involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.