In this report the major locus for Puccinia psidii rust resistance, Ppr1, was positioned on the reference genetic map for Eucalyptus. Additionally, its position was validated by association genetics in a related and two unrelated pedigrees involving different Eucalyptus grandis resistant trees crossed to individuals of two other species, Eucalyptus tereticornis and Eucalyptus camaldulensis. These results are consistent with the hypothesis that Ppr1 controls a large proportion of the variation for rust resistance, strengthening its role as a major locus in Eucalyptus and providing its unequivocal genomic position on linkage group 3. A localized map with 19 microsatellite loci was built around Ppr1. Multiallelic profiles were observed at several mapped microsatellites suggesting recent tandem duplications in the genomic landscape surrounding Ppr1. Markers EMBRA125 and EMBRA1071 flank Ppr1 at 9.5% and 7% recombination, respectively, and were found to be in linkage equilibrium in a E. grandis breeding population, consistent with the expectations in outcrossed Eucalyptus. Their potential use for MAS will specifically be directed to identifying resistant offspring of P. psidii resistant parent trees that are heterozygous at Ppr1. In these circumstances, a significant amount of LD is expected to occur between specific alleles at flanking microsatellites and the resistance allele at Ppr1. Moreover, the positional information of Ppr1 paves the way for prospective undertakings in this genomic region with the upcoming availability of a draft genome for E. grandis.