Phylogenetic analyses can provide an accurate identification for endangered species, which is a prerequisite for their conservation. Understanding how threats shape the current realized niche of declining species can effectively improve conservation policies. In this study, we used molecular data to identify the real Eleutharrhena macrocarpa, a critically endangered species in Yunnan, China. A niche reduction approach was used to model its range change by predicting the historic and current distributions. Our subfamily-wide phylogenetic analyses based on five plastid DNA regions indicate that the E. macrocarpa with pinnate-nerved leaves is real and is a member of Tiliacoreae, whereas the so-called E. macrocarpa with triplinerved leaves is actually Haematocarpus subpeltatus, which is for the first time reported to be distributed in China. Our subsequent analyses of Tiliacoreae using seven plastid and two nuclear DNA regions further support Eleutharrhena as a distinctly monotypic genus and as sister to Pycnarrhena. Among the four prevalent barcodes in plants, three plastid DNA fragments (rbcL, matK, trnH-psbA) failed to discriminate E. macrocarpa from Pycnarrhena; however, nuclear ribosomal internal transcribed spacer (ITS) regions could well recognize this endangered species. The distributional range of E. macrocarpa has undergone a dramatic contraction over the last 100 years and may further shrink southwestwards in the future. This dramatic range contraction might be associated with habitat loss due to increasing drought and expansion of rubber plantation. We point out the need for in situ conservation of E. macrocarpa populations, and suggest to establish a large nature reserve in southern and western Yunnan to effectively protect E. macrocarpa and other declining species that exhibit similar distribution and habitat requirements. This study highlights the significance of taxonomy and molecular phylogenetics in biological conservation.