Perilla rust is a damaging disease in perilla cultivation in Korea. Its causal agent was identified as Coleosporium plectranthi based on descriptions of morphological characteristics of spores and spore-producing fruiting structures (in uredinial and telial stages from perilla and in aecial stage from the alternate host pine) collected in 15 locations in Korea during the disease survey from 2004 to 2006. These characteristics were yellow or orange uredinium; globose or ellipsoid urediniospore of 20.8 μm×18 μm in size; verruca of 0.3 mm×1.2 mm; orange telium; one-celled, oblong ellipsoid teliospore of 63.1 μm×19.7 μm with one-layered crusts or four-celled (when mature), internal basidium of 64.2 μm×19.7 μm; ellipsoid to globoid basidiospore of 20.3 μm×12 μm; type 2 spermogonium; yellow, broadly ellipsoid peridial cell of 35.6 μm×23.1 μm; and broadly ellipsoidal or subglobose aeciospore of 25.9 μm×18.8 μm. Phylogenetic analysis of 28S rDNA sequences revealed the closest relatedness to those of the genus Coleosporium, a monophyletic group distinguished from other rust fungi and divided into two main lineages, one of which was C. plectranthi grouped with high bootstrap value (96%). In pathogenicity test, both aeciospores and urediniospores caused rust development on perilla leaves. This is the first description of C. plectranthi causing perilla rust with the first findings of its telial stage on perilla and the first rust disease on the aecial host in Pinus densiflora. These aspects would provide basic information for the development of control measures of the disease.