A rust resistance gene is used as a target to experience map-based cloning in a typical interspecific, highly polyploid, aneuploid sugarcane cultivar (Saccharum spp., 2n= 100 to 130). Bulk segregant analysis with AFLP markers allowed surrounding the target resistance gene with 8 AFLP markers, the closest being located at 2 cM on each side of the gene. These two AFLP markers were cloned and mapped on sorghum, suggesting a local inversion between sugarcane and sorghum. Several RFLP loci located in the target region in sorghum maps were then mapped on sugarcane. They allowed surrounding the gene with markers located at 0.3 and 0.6 cM on each side. These markers were also used to screen a partially ordered sorghum BAC library, enabling us to build a sorghum BAC contig covering the homeologous target region in sorghum. If synteny is conserved at a fine level in this region, this contig should also cover the region that encompasses the rust resistance gene in sugarcane.