Pterocarya serrata C.K.Schneid., originally described in 1912, has long been treated as a synonym of Cyclocarya paliurus (Batal.) Iljinsk. in Plants of the World Online (POWO). Based on an integrative framework combining ploidy determination, morphometric analyses, ecological niche comparisons, and molecular phylogenetics of mixed-ploidy populations, together with extensive herbarium and field investigations, we formally reinstate Pterocarya serrata as a distinct species within the genus Cyclocarya, recognizing three synonyms. Our results reveal clear phenotypic divergence and genetic differentiation between C. serrata and C. paliurus, which have evolved into separate evolutionary lineages. These findings refute the traditional treatment of Cyclocarya as a monotypic genus. Furthermore, we present the first comprehensive morphological descriptions, distribution records, and taxonomic notes for both C. serrata and C. paliurus, thereby advancing the systematic understanding of Cyclocarya.