The 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 production of forest products, carbon sequestration, biofuels production, and bioremediation. The disease is caused by a complex of species that comprise Melampsora medusae f. sp. deltoidis (Pucciniomycotina; Pucciniomycetes; Pucciniales; Melampsoraceae). This heteroecious pathogen requires alternation on two different hosts, poplar and several conifers, 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. deltoidis is pathogenic on poplars in the Aigeros section (e.g. Populus deltoides) but M. occidentalis is pathogenic on poplars in the Tacamahaca section (e.g. Populus balsamifera, P. trichocarpa). Both rusts can alternate on larch, pines and Douglas-fir. A hybrid between these two species has a broader host range than either parental species and can attack 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. deltoidis 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 pathogens in these economically and ecologically important trees.