<p>Over-splitting of plant taxa refers to the splitting of plant entities into an excess of small taxonomic units. The over-splitting of intraspecific taxa (e.g., variety) can challenge the legal delimitation of threatened species and the effective allocation of limited conservation resources. The dove tree (<i>Davidia involucrata</i>) has two varieties, namely <i>D. involucrata</i> var. <i>involucrata</i> and <i>D. involucrata</i> var. <i>vilmoriniana</i>, which are distinguished mainly by the appearance of trichomes on the leaf back or not. This traditional classification remains debated because of its minor visible morphological differences and the lack of genetic evidence. We collected range-wide morphological (trichome density and geometric morphometrics), whole-genome resequencing (genome-wide SNPs), and type specimen data to examine taxa boundaries. The leaf trichomes of this species complex are simple (unbranched) non-glandular, and the density varies continuously. Geometric morphometric analysis demonstrated that the leaf shape cannot be unambiguously separated. Within the phylogenetic tree, the two putative taxa were mixed. Population genetic structure analyses consistently revealed three well-supported genetic clusters, whose geographic distribution did not match those of the two putative taxa. Collectively, <i>D</i>. <i>involucrata</i> var. <i>vilmoriniana</i> is not genetically or morphologically differentiated from <i>D. involucrata</i> var. <i>involucrata</i>. The type specimens of the two varieties were collected from distant areas, indicating that their splitting might be caused by collection bias. Our study highlights the importance of integrative taxonomy approaches in unravelling the over-splitting of intraspecific ranks and providing empirical support for the abandonment of over-splitting varieties in wild plant taxonomy.</p>