Puccinia menthae is highly variable, with several varieties and variants within varieties. Two principal groups of races, nominated spearmint rust and peppermint rust, have been recognized according to their host range on commercially-important Mentha species, yet both belong to the same variety, P. menthae var. menthae. Ten collections of P. menthae teliospores from four Mentha species in Victoria, Australia, were examined using light microscopy and SEM. The teliospores from M. spicata, M.×cordifolia and M. suaveolens, all hosts to spearmint rust, were verrucose with two equally-sized cells, whereas those from M.×piperita, host to peppermint rust, were generally smooth-walled, and the apical cell was larger and thicker-walled than the basal cell. Fifteen isolates of P. menthae collected from four Mentha species in Victoria were assessed for genomic variation using RAPD analysis and PCR-generated length polymorphism of the ITS region of rDNA. Six out of 113 RAPD primers amplified reproducible marker profiles, 58 polymorphic bands were scored and simple matching distances were computed between the isolates. UPGMA cluster analysis was used to produce a dendrogram and non-metric multi-dimensional scaling to produce a two-dimensional map of the isolates. The spearmint rust and peppermint rust isolates clustered into two non-overlapping groups, providing good evidence that there is limited gene flow between them. All isolates had the same sized ITS fragments. The taxonomic implications of these results are discussed and it is suggested that the peppermint and spearmint rusts should be accorded separate varietal or specific status.