Pre-harvest sprouting (PHS) is a major problem of wheat production system due to its direct detrimental effects on wheat yield, end-use quality and seed viability. In Canada, PHS is estimated to cost ~$100 million annually to spring wheat alone. Although growing wheat cultivars those can resist PHS has long been considered the most promising approach to alleviate the associated risks, development of PHS resistant cultivars has been hindered due to the lack of complete understanding, complexity of the resistance mechanism and unavailability of the molecular markers. Therefore, to identify the PHS resistance loci and their markers, a doubled haploid mapping population derived from a cross between PHS susceptible cv AAC Innova and resistant cv AAC Tenacious was utilized. It was phenotyped for PHS in 2018 and 2019 in mist chambers followed by SNP genotyping and quantitative trait loci (QTL) mapping. QTL mapping identified three PHS QTLs on wheat chromosomes 2D, 3B and 3D. Comparison of 2D genetic interval with 2D reference genome sequence identified an ARGONAUTE gene. We also identified a single nucleotide polymorphism (SNP) marker in this gene. Results of present study indicate a role of epigenetic factors in PHS resistance perhaps through the modulation of DNA methylation.