The very high resistance to rice yellow mottle virus observed in the two rice varieties Gigante (Oryza sativa) and Tog 5681 (O. glaberrima) is monogenic and recessive. Bulked segregant analysis was carried out to identify AFLP markers linked to the resistance gene. Mapping of PCR-specific markers, CAPS and microsatellite markers on 429 individuals of an IR64 × Gigante F 2 population pinpointed this resistance gene on the long arm of chromosome 4 in a 3.7-cM interval spanned by PCR markers. These markers also flanked the resistance gene of the O. glaberrima accession Tog 5681 and confirmed previous allelism tests. The rarity of this recessive natural resistance was in line with a resistance mechanism model based on point mutations of a host component required for cell-to-cell movement of the virus. Preliminary data on the genetic divergence between the two cultivated rice species in the vicinity of the resistance locus suggested that two different resistance alleles are present in Gigante and Tog 5681. A large set of recombinants is now available to envisage physical mapping and cloning of the gene.