Caryodaphnopsis is a small genus of the Lauraceae family with disjunct distribution in tropical Asia and tropical America. Taxa from each region form a well-supported monophyletic clade. However, the species circumscription in Asian Caryodaphnopsis remains ambiguous due to few and generally unstable morphological characters used for classification. To address this, we conducted an integrative taxonomy of the Asian clade. We investigated 13 populations, sampled 57 accessions covering the entire taxonomic diversity, geographic range, and morphological variation in Asia, and reconstructed a new phylogeny using single-nucleotide polymorphisms. We obtained a well-resolved phylogeny of the Asian Caryodaphnopsis. The first diverged clade consists of three species endemic to lowland forests. The second (largest) clade (eight species in total) mainly occurs in limestone mountain forests and has a double-layered lower leaf epidermis morphology of type 2 (less complete roomy with closed “roof”) and type 3 (complete roomy with closed “roof”). Based on the diagnostic morphological characters, distinct distributional ranges, and monophyly of each clade, we recognize 12 species in the Asian Caryodaphnopsis, including three new species: C. cangyuanensis sp. nov., C. hekouensis sp. nov., and C. rubrinervis sp. nov. We also reinstate C. latifolia, and re-circumscribe the widespread C. tonkinensis and other species based on fruit and inflorescence morphology and molecular evidence.