Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security. Genetic resistance can reduce crop losses in the field and can be selected through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici (Pst). This highlights the need to (i) identify genes that alone or in combination provide broad-spectrum resistance, and (ii) increase our understanding of the underlying molecular modes of action. Here we report the isolation and characterisation of three major yellow rust resistance genes (Yr7, Yr5, and YrSP) from hexaploid wheat Triticum aestivum, each having a distinct recognition specificity. We show that all three genes are genetically linked; Yr5 is distinct from Yr7, whereas YrSP is a truncated allele of Yr5 with 99.8% sequence identity. All three Yr genes belong to a complex resistance gene cluster on chromosome 2B encoding nucleotide-binding and leucine-rich repeat proteins (NLRs) with a non-canonical N-terminal zinc-finger BED domain that is distinct from those found in nonNLR wheat proteins. We developed diagnostic markers for haplotype analysis and marker-assisted selection to help expedite the stacking of the non-allelic Yr genes. The relationship of these three distinct Yr loci will inform future hypothesis-driven engineering of novel recognition specificities.