Uromyces japonicus is an autoecious leaf rust of Allium victorialis sensu lato. The rust forms concentric sori on the adaxial surface of host leaves. This fungus is a potential pathogen for economically important Allium plants. Initially, we observed in planta fungal structures using newly developed whole-leaf fluorescent imaging method to evaluate the rust lesion formation process. We then confirmed conspecificity of Japanese and European populations by comparing the morphological characteristics and rDNA sequences. In addition, we estimated phylogenetic relationships among rust fungi on Allium plants. In this study, we designate an epitype of U. japonicus based on fresh specimens from Japan.