Yellow mosaic virus, YMV, causes one of the most severe of biotic stresses in Vignas, an important group of pulse crops. The viral disease is transmitted through the white fly, Bemicia tabaci, and the yield of the plants is affected drastically. YMV-tolerant lines, generated from a single YMV-tolerant plant identified in the field within a large population of the susceptible cultivar T-9, were crossed with T-9, and F1, F2 and F3 progenies raised. The different generations were phenotyped for YMV-reaction by forced inoculation using viruliferous white flies. A monogenic recessive control of YMV-tolerance was revealed from the F2 segregation ratio of 3:1 (susceptible: tolerant), which was confirmed by the segregation ratio of the F3 families. Of 24 pairs of resistance gene analog (RGA) primers screened, only one pair, RGA 1F-CG/RGA 1R, was found to be polymorphic among the parents. Selected F2 individuals and F3 families were genotyped with the polymorphic RGA primer pair and the polymorphism was found to be linked with YMV-reaction. This primer pair amplified a 445bp DNA fragment only from homozygous tolerant and the heterozygous lines. The 445bp marker band was sequenced and named 'VMYR1'. The predicted amino acid sequence showed highly significant homology with the NB-ARC domain present in several gene products involved in plant disease resistance, nematode cell death and human apoptotic signaling. To the best of our knowledge, this is the first report of YMV-resistance linked DNA marker development in any crop species using segregating populations. This YMV-resistance linked marker is of potential commercial importance in resistance breeding of plants. © 2004 Kluwer Academic Publishers.