<p>Biodiversity status assessments are typically conducted on a regional basis. Consequently, there are numerous species that are rare in one region but ubiquitously present in another country or administrative region. Correctly assessing the conservation status and value of such “endangered species” is essential to achieve better biodiversity conservation through the appropriate and efficient use of socioeconomic resources. A comparative genomic analysis was conducted on <i>Torenia concolor</i>, which is widely distributed in Southeast and East Asia, but has a limited population in Japan, specifically on Amami Oshima Island. This population has not yet been established as a conservation priority due to the possibility that it may have originated from cultivated plants. We hypothesized that the population was not due to a human-induced distribution; indeed, our findings indicate that the Amami Oshima population is derived from a natural distribution and is phylogenetically unique, retaining comparable genetic diversity with more abundant populations and exhibiting no increase in deleterious variations in their genome. These findings highlight the unique conservation significance of the Amami Oshima population. Furthermore, the findings suggest that this population, being genetically robust, may be sustainably conserved through minimal intervention strategies, such as maintaining current habitat conditions and monitoring population size, as the accumulation of deleterious mutations is comparable to that of the Taiwanese population. This study highlights the importance of accurate assessment of genomic status and contributes to a broader understanding of conservation strategies for regionally rare species.</p>