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A rust fungus was found on the leaves of Euphorbia helioscopia during a field study in Pakistan. Previously, Melampsora euphorbiae, M. euphorbiae-gerardianae and M. helioscopiae have been reported on E. helioscopia, the first two of which are also known from Pakistan. Morphological observations of the newly collected rust samples detected some differences from the previously described Melampsora species on E. helioscopia. The molecular analysis of the ITS and LSU sequences also detected that the rust is different from the previously reported rusts described from E. helioscopia. Based on both morphological comparisons and sequence analysis, the rust is described here as M. pakistanica sp. nov. This species could have potential as a bio-control agent against its host plant—E. helioscopia—which is a weed of wheat fields in Pakistan and elsewhere in the world.