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Allanites from the Japanese island arc are not necessarily the same as those from other countries of the world. The study of minerals occurring in the Japanese islands context is integrated into “island arc mineralogy”, which concerns the following space-time continuum: (1) the present island arc, (2) the post-Paleozoic rocks, (3) subduction-related magmatism, (4) volcanic front, (5) tectonic discontinuities, and (6) an abundant variety of minerals, their paucity and characteristic accessory minerals. “Island arc mineralogy” of allanites from Japan is functionally related to (1), (2), (3) and (6). This paper focuses on tectonic setting (intracontinental settings,island arcs, and continental margin), formation age and a variety of host rock types containing allanite, crystal chemisry of REE-rich epidote group minerals, particularly allanite, and geochemical role of their chemical composition, crystal structure and mineral inclusion.