Middle Devonian conodonts from the Si Phai section in NE Vietnam are described. The section ranges from the Middle Devonian ensensis to timorensis conodont zones to the Late Devonian rhomboidea conodont Zone. A rich overall assemblage is described, including 27 taxa of species or subspecies rank and 11 taxa described in an open nomenclature. Among the dominant Polygnathus forms, four new taxa are described: Polygnathus linguiformis saharicus subsp. nov., Polygnathus linguiformis vietnamicus subsp. nov., Polygnathus rhenanus siphai subsp. nov., and Polygnathus xylus bacbo subsp. nov. Conodont assemblages are attributed to polygnathid, polygnathid-klapperinid, and klapperinid conodont biofacies representing hemipelagic to pelagic environments. The klapperinid biofacies, unreported in the previous literature, are here attributed to offshore areas of the external shelf. The taxonomic compositions of the studied conodont assemblages, as well as their CAI characteristics (CAI 4–5), suggest a palaeogeographic affinity of the studied strata to the Chinese Devonian Guangxi Basin, and the South China Terrane in general. Furthermore, the conodont biofacies and the palaeogeographic distribution of the fauna are discussed.