Barley mild mosaic virus(BaMMV), transmitted by the soil-borne protistPolymyxa graminis, has a serious impact on winter barley production. Previously, the BaMMV resistance generym15was mapped on chromosome 6HS, but the order of flanking markers was non-collinear between different maps. To resolve the position of the flanking markers and to enable map-based cloning ofrym15, two medium-resolution mapping populations Igri (susceptible) × Chikurin Ibaraki 1 (resistant) (I × C) and Chikurin Ibaraki 1 × Uschi (susceptible) (C × U), consisting of 342 and 180 F2plants, respectively, were developed. Efficiency of the mechanical inoculation of susceptible standards varied from 87.5 to 100% and in F2populations from 90.56 to 93.23%. Phenotyping of F2plants and corresponding F3families revealed segregation ratios of 250 s:92r (I × C,χ2= 0.659) and 140 s:40r (C × U,χ2= 0.741), suggesting the presence of a single recessive resistance gene. After screening the parents with the 50 K Infinium chip and anchoring corresponding SNPs to the barley reference genome, 8 KASP assays were developed and used to remap the gene. Newly constructed maps revealed a collinear order of markers, thereby allowing the identification of high throughput flanking markers. This study demonstrates how construction of medium-resolution mapping populations in combination with robust phenotyping can efficiently resolve conflicting marker ordering and reduce the size of the target interval. In the reference genome era and genome-wide genotyping era, medium-resolution mapping will help accelerate candidate gene identification for traits where phenotyping is difficult.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11032-021-01270-9.