Hantaviruses are zoonotic RNA viruses that cause hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome, posing significant public health risks. This study reports the identification and genomic characterization of Ulleung virus (ULLEV), a newly discovered genetic lineage of Orthohantavirus jejuense harbored by Crocidura utsuryoensis, a shrew species endemic to Ulleung Island, Republic of Korea. In 2009, a surveillance effort involving 62 shrews revealed a molecular prevalence of 64.5%. Metagenomic next-generation sequencing identified four viral variants, with ULLEV Cu09-33 fully characterized. Comparative genomic and phylogenetic analyses confirmed ULLEV as a distinct subtype within O. jejuense and suggested that ULLEV and Jeju virus (JJUV) share a common ancestor, with divergence shaped by long-term co-evolution with their hosts and geographic isolation. Haplotype network analysis of mitochondrial DNA detected eight unique haplotypes in C. utsuryoensis, distinct from C. shantungensis populations, indicating genetic isolation. While incongruences among the tripartite genomes of ULLEV and JJUV suggested independent evolutionary trajectories, evidence for reassortment remains insufficient. These findings highlight the ecological significance of geographically isolated environments as reservoirs for unique hantavirus lineages and underscore the need for expanded genomic surveillance and phylogenetic studies to assess the zoonotic potential and public health implications of ULLEV.