The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance geneLr9, which was introduced into bread wheat from the wild grass speciesAegilops umbellulata2. We established thatLr9encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheatLr9introgression line and the putativeAe. umbellulata Lr9donor enabled us to assemble the ~28.4-MbLr9translocation and to identify the translocation breakpoint. We likewise clonedLr58, which was reportedly introgressed fromAegilopstriuncialis3, but has an identical coding sequence compared toLr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.