Abstract
BACKGROUND: The taxonomy of Paphiopedilum-a diverse group of slipper orchids-has long posed challenges due to high morphological variability and conflicting phylogenetic signals. Despite intensive research, a clear and stable infrageneric classification remains unresolved. RESULTS: We present an integrative phylogenetic framework based on multiple nuclear low-copy genes (XDH, PHYC, LFY, RAD51, ACO, DEF4), ITS and plastid (matK) sequences, supported by morphological and biogeographical data. Our analyses consistently recovered monophyletic clades corresponding to both historically recognized and newly proposed lineages. Phylogenetic incongruence observed both between different nuclear loci and between nuclear and plastid phylogenies suggests a reticulate evolutionary history shaped by ancient hybridization events and incomplete lineage sorting. Biogeographic reconstructions place the genus' origin in mainland of Southeast Asia during the Miocene, with subsequent radiation influenced by climatic and geological events. As a result, we propose a revised classification recognizing three genera-Parvisepalum, Brachypetalum, and Paphiopedilum s.str.-with the latter subdivided into six subgenera. CONCLUSIONS: This study provides the most comprehensive phylogenetic and taxonomic treatment of Paphiopedilum to date. Our framework reflects evolutionary relationships more accurately than previous systems and offers a stable basis for future research in orchid systematics, conservation, and evolution.