Background <p>Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne disease caused by the SFTS virus (SFTSV). In Japan, the highest number of SFTS cases has been reported in the Miyazaki Prefecture. Despite previous genomic studies, the regional genomic diversity of SFTSV in Japan remains poorly characterized at the prefectural level. Hence, we aimed to analyze the whole genome sequencing of SFTSV strains collected in the Miyazaki Prefecture to assess their genomic diversity.</p> Methods <p>Epidemiological data from patients were analyzed, and amplicon-based whole genome sequencing of SFTSV was performed using serum or plasma samples collected between 2012 and 2023 in the Prefecture. The resulting sequences were used to construct a phylogenetic tree, and the distribution of SFTSV genotypes was analyzed according to the presumed regions of infection.</p> Results <p>The phylogenetic analysis revealed that four genotypes of SFTSV were present in the Prefecture, including currently unclassifiable genotypes and a novel subgenotype named J4. Analysis of the geographic distribution of each genotype revealed an association between genotypes and presumed regions of infection. Notably, potential genetic reassortment and recombination events were confirmed in Japanese strains.</p> Conclusions <p>This study provides the largest whole genome sequencing of SFTSV conducted in Japan to date and confirms that SFTSV genotypes in the Miyazaki Prefecture exhibits strong regionality. Accordingly, we hypothesized that the dispersion of SFTSV through ticks and wild animals may be relatively limited. SFTSV genome analysis may help to estimate infection locations, particularly for cases with an unclear exposure history.</p> Graphical Abstract <p></p>