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Japan is one of the world’s 34 biodiversity hotspots, according to Conservation International (CI). The methods used by various organisations to define priorities differ, however, and all have weaknesses when trying to identify hotspots at finer resolutions. The goal of this thesis is to investigate how biodiversity hotspots in Japan could be revealed and mapped in order to encapsulate conservation elements of biodiversity in practical ways and at various scales. Bioquality is a term that emphasises the concentration within a community of elements of biodiversity with high conservation value. It evaluates the global rarity and taxonomic distinctiveness of plant species or infra-specific taxa using four Star categories. At a plant community level, the Genetic Heat Index (GHI), which is a standardised global range size rarity score, is calculated using weighted Star statuses of species in the community. Bioquality hotspots are assessed here for the first time for the flora and vegetation in Japan – and for temperate Asia – by categorising the Japanese flora into Stars and by applying GHI to survey data and literature-based sources. Keys to Stars are developed for the Japanese flora, with adjustments for variability in species geographic range size information and for taxonomic relatedness. A Flora of Japan (FOJ) database was compiled as a BRAHMS database, containing 8,262 accepted names (30,656 taxon names in total, including synonyms) in 258 families – the first full database of Japanese vascular plants. A total of 7,145 taxa are assigned Stars; from the rarest to the widespread class, there are 884 Black, 756 Gold, 833 Blue, and 4,672 Green Star taxa, confirming that Japan as a whole contains a high proportion of globally rare taxa (23% taxa in Black or Gold). A protocol for calibrating the weight of Stars based on species geographic range is developed based on fine-resolution distribution maps within Japan and coarse–resolution Taxonomic Database Working Group (TDWG) code information. The protocol optimises calculation for temperate regions. The first ever bioquality hotspot maps of Japan are produced using two independent data sources on species distribution at national level: 1) 50 botanical prefectures using 4,830 species from the FOJ database; 2) 1,418 Horikawa ‘geoquadrats’ (0.1° latitude by 0.15° longitude grid) maps covering 829 species. The Ryukyu Islands and Ogasawara Islands are identified as bioquality hotspots, and high mountain ranges in mainland Japan are predicted to contain areas potentially high in GHI; the spatial patterns of GHI are generally concordant between maps of different resolutions. These findings highlight that bioquality assessment can be applied meaningfully at various spatial resolutions. Using field sampling data and existing literature, three study sites are further investigated on a local level: 1) the satochi-satoyama landscape, the current national priority area for biodiversity conservation; 2) various vegetation types of Okinawa-jima Island, the Ryukyu Islands; and 3) the Utaki sacred groves within the predicted hotspot of the Ryukyu Islands. The Ryukyu Islands are confirmed to contain bioquality hotspots within many individual sites, while there was generally low GHI across the satochi-satoyama landscape. The field study outcomes, together with a gap analysis of the existing coverage of protected areas, highlight three important points that are directly relevant to national biodiversity conservation planning: 1) the Ryukyu Islands urgently need newly designated protected areas; 2) the satochi-satoyama landscape conservation should redirect its focus on cultural benefits to the public; 3) the existing protected areas, particularly on mountain areas, need re-evaluation in terms of upgrading their status in light of the bioquality assessment.