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Taxonomical re‐examination of the Phyllosticta species parasitic fungi on coniferous trees (Cupressaceae) in Japan was conducted based on current criteria, such as morphological and cultural characteristics, phylogenetic relationship and pathogenicity. Phylogenetic analyses revealed several clades composed of plant pathogens isolated from a specific host as well as clades composed of endophytic species isolated from various Cupressaceae trees. Each clade was recognized as a species from the morphological characteristics and other features, respectively. Five species of Phyllosticta sensu stricto were recognized, and two of them were newly recorded in Japanese mycoflora. Furthermore, new comibination P. pilospora and its epitype are proposed. The epitype and ex‐type strain are also proposed for P. cryptomeriae in this study.