Deep-water facies sections have advantages of recording complete information across the Permian-Triassic boundary (PTB). Here we present a detailed study on the conodont biostratigraphy and carbon isotope profile ranges from the Wuchiapingian-Changhsingian boundary (WCB) to the PTB of two deep-water facies sections at Zhuqiao and Shiligou in the Middle Yangtze region, western Hubei, South China. Fifteen species and three genera are identified. Eight conodont zones are recognized, in ascending order, they are the Clarkina orientalis, C. wangi, C. subcarinata, C. changxingensis, C. yini, C. meishanensis, Hindeodus parvus and Isarcicella isarcica zones. The onset of deposition of the deep-water siliceous strata of the Dalong Formation in western Hubei began in the Late Wuchiapingian and persisted to the Late Changhsingian. Carbon isotope negative excursions occur near both the WCB and PTB in both sections. The WCB delta C-13(carb) negative excursion is in the C. orientalis and C. wangi zones. The PTB delta C-13(carb) negative excursion began in the C. yini Zone and extended to the I. isarcica Zone. The absence of several Changhsingian zones may indicate the difficulty of extracting conodonts from siliceous strata or the presence of an intra-Changhsingian hiatus.