Salix and Populus are the most important genera of the family Salicaceae and most widely have been planted for farmland sheltering, wood and biomass production including biomass of pulp, fuel and forage. In addition, they are used for making baskets and cages, ornamentation and windbreaks. Recently, many clones of Salix and Populus are grown in short-rotation coppice (SRC) plantations for renewable energy. One of the major problems encountered in growing willow and poplar is the rust disease caused by Melampsora . This rust could cause losses of 30-40% dry matter and 60% stool death in susceptible clones. In order to identify species of Melampsora , twenty-two isolates were collected from Isfahan province. Details of macroscopic and microscopic characteristics in cooperate with molecular methods were used to identify the species of these isolates. Three species of Melampsora , including; M. salicis-albae on Salix alba , M. euonymi-capraearum on S. caramanica and M. magnusiana on Populus alba have been identified and the latter’s species are reported for the first time from Iran . Most isolates on Salix sp. identified as M. salicis-albae by morphological studies. Isolates KH1 and KH2 ( S. caramanica) are matrix nova for M. euonymi-capraearum . The other isolates which were colleced on P. alba identified as M. magnusiana . Urediniospores with evenly echinulate surface separate M. magnusiana from other species that are reported on poplar in Iran . DNA of all isolates was extracted by Abbasi et al . method. Two specific primers for Basidiomycetes, ITS1-F and ITS4-B were used and all isolates showed an 800-830 bp band. In order to study genetic variation three restriction enzymes, Eco RI, Hae III and Alu I were used. The restriction sites in the amplified DNA fragment were the same that showed PCR-RFLP couldn't determine the variation between species or in species. So this method isn't a reliable method for identifying parasitic Melampsora species on poplar and willows in Isfahan province. Amplified DNA fragment of urediniospores of four isolates on salix sp., one isolate on populus sp. and Caeoma sp. collected from Hamadan were sequenced. Then sequences
