Two sequence-tagged site (STS) markers for the wheat yellow rust resistance (R) gene Yr5 have been derived through the identification and characterization of linked amplified fragment length polymorphisms (AFLPs). The sequences of the 2 AFLP markers partially overlap with one another, but belong to discrete loci S19M93-140 completely cosegregates with Yr5, whereas S23M41-310 maps at a distance of 0.7 cM. The DNA sequence of S23M41-310 shows significant homology with the 3' end of nucleotide-binding site (NBS) - leucine-rich repeat (LRR) - type R-genes, in particular with orthologues of the rice bacterial blight R-gene Xa-I. The distinct genetic location of the 2 AFLP loci suggests that Yr5 falls within an R-gene cluster. Because neither sequence forms part of a detectable transcription product, we propose that the Yr5 R-gene cluster includes R-gene analogues and pseudogenes. A Yr5 flanking simple sequence repeat (SSR) marker has also been identified, which allows Yr5 to be effectively incorporated, along with other R-genes for yellow rust, into elite wheat genetic backgrounds, through marker-assisted selection.