The northern parts of Yunnan belong to 'Mountains of SW China' biodiversity hot spot, one of the most species-rich areas on earth. Although some progress, relatively little attention has been given to explore the evolutionary history of the fern diversity of this hot spot. According to recent progress, Yunnan exhibits the heterogeneity of species diversity among regions. In this study, we focused on the Dehong Dai-Jingpo Autonomous Prefecture, an overlooked area in western Yunnan geographically and geologically, which is connected to SE Tibet and NE Myanmar; thus, the flora of this region will likely share several unique taxa, but this pattern may be obscured by the lack of reported distributions. To examine this, we conducted floristic investigation targeting rare species shared between Dehong and adjacent areas inLepisorus. We performed morphological, phylogenetical, and biogeographical analyses with the accessions obtained.Lepisorus cespitosuswas firstly found in Dehong, which was previously only known from the type location in SE Tibet. Our analyses revealed thatL. cespitosusis a lineage morphologically and phylogenetically isolated from all other sections ofLepisorus.Divergence time estimates and ancestral area reconstruction supported thatL. cespitosusis a relict species survived in this region since the Late Miocene. Our results showed the affinity in the flora between western Yunnan and SE Tibet and supported the hypothesis that this region has served as a climate refugia for relict species during the Cenozoic. Thus, we propose that more attention should be given to floristic investigation in this area and adjacent regions.