The Rrs2 gene confers resistance to the fungal pathogen Rhynchosporium secalis which causes leaf scald, a major barley disease. The Rrs2 gene was fine mapped to an interval of 0.08 cM between markers 693M6_6 and P1D23R on the distal end of barley chromosome 7HS using an Atlas (resistant) x Steffi (susceptible) mapping population of 9,179 F(2)-plants. The establishment of a physical map of the Rrs2 locus led to the discovery that Rrs2 is located in an area of suppressed recombination within this mapping population. The analysis of 58 barley genotypes revealed a large linkage block at the Rrs2 locus extending over several hundred kb which is present only in Rrs2 carrying cultivars. Due to the lack of recombination in the mapping population and the presence of a Rrs2-specific linkage block, we assume a local chromosomal rearrangement (alien introgression or inversion) in Rrs2 carrying varieties. The variety analysis led to the discovery of eight SNPs which were diagnostic for the Rrs2 phenotype. Based on these SNPs diagnostic molecular markers (CAPS and pyrosequencing markers) were developed which are highly useful for marker-assisted selection in resistance gene pyramiding programmes for Rhynchosporium secalis resistance in barley.