Melastoma dendrisetosum is an extremely narrowly distributed taxon endemic to the Diaoluo Mountain region in Hainan, China, and was recently taxonomically incorporated under a widespread species, M. sanguineum. Based on its distinct morphological traits, especially the indumentumon the hypanthium, we propose that it should represent a distinct species. In this study,we sequenced six partial nuclear genes and two chloroplast intergenic spacers of M. dendrisetosum and three other morphologically similar species, M. sanguineum, M. penicillatum, and M. normale, to clarify its taxonomic status. M. dendrisetosum exhibited an extremely low level of genetic diversity, and was well separated from the three other species with no shared haplotypes at all six nuclear genes, supporting the hypothesis that it is a distinct species. This finding was also supported by the Bayesian clustering-based STRUCTURE analysis, phylogenetic analysis, and Bayesian species delimitation analysis. We further propose that if a formal assessment were performed, M. dendrisetosum would be categorized as ‘Critically Endangered’ under the IUCN criteria, due to its extremely small population and declining habitat quality. We suggest that the conservation of M. dendrisetosum be prioritized, and road construction in its range should be avoided, to protect this distinct and critically endangered species.