Poplar leaf rust is the most devastating and widespread disease of poplars worldwide and has a severe impact on current and future poplar plantations used for wood and biofuel production, carbon sequestration, and phytoremediation. The disease is caused by members of the Melampsora medusae f. sp. tremuloidae species complex (Pucciniomycotina; Pucciniomycetes; Pucciniales; Melampsoraceae). This heteroecious pathogen requires alternation between poplar and a conifer of the Pinaceae family to complete its life cycle. Pathogens in this complex are usually host-specific on the telial (poplar) but not on the aecial (conifer) host: Melampsora medusae f. sp. tremuloidae is pathogenic on poplars in the Populus section (e.g. Populus tremuloides) but its close relative M. medusae f. sp. deltoidis is pathogenic on poplars in the Aigeros section (e.g. Populus deltoides) and M. occidentalis is pathogenic on poplars in the Tacamahaca section (e.g. Populus balsamifera, P. trichocarpa). These rusts can alternate on larch, pines and Douglas fir. Hybridization among these rusts can increase host range and threatens commercial hybrid poplars that were previously resistant. There is a need to further our understanding of the Melampsora species complex in order to develop new management approaches. The genome sequencing of Melampsora medusae f. sp. tremuloidae is part of a larger effort, the Pathobiome Database for Bioenergy Trees Project that aims to sequence the genomes of multiple pathogens that share the same host trees in order to identify common and unique genomic signatures. This data will be used to create a database that will help the development of tools for the detection, monitoring and surveillance of fungal pathogens with the potential to cause infection of these economically and ecologically important trees.