Conodont biostratigraphic and high-precision U-Pb isotope data are presented for the Permian-Triassic transition in three limestone hills, Gua Bama, Gua Panjang and Gua Sei, in the Malay Peninsula. Gua Bama yielded conodonts representating the <i>Clarkina orientalis</i>, <i>Clarkina wangi</i> and <i>Clarkina subcarinata</i> zones and the Wuchiapingian-Changhsingian stage boundary is identified for the first time in Malaysia. The Wuchiapingian subspecies <i>Hindeodus julfensis wardlawi</i> Kozur is elevated to species level, <i>H. wardlawi</i>, and evolved to the Changhsingian species <i>Hindeodus julfensis</i> Sweet and then <i>Hindeodus changxingensis</i> Wang. Distinguishing features and a new phylogeny of species of the genera <i>Hindeodus</i> and <i>Isarcicella</i> in the Late Permian-Early Triassic are presented. A new CA-TIMS high-precision U-Pb age of 253.70 ± 0.06 Ma for zircon from a tuff layer 6.5 m above the Wuchiapingian-Changhsingian boundary and in the lower part of the <i>Clarkina subcarinata</i> zone is reported. Conodont faunas from Gua Panjang represent the <i>Clarkina changxingensis-Hindeodus praeparvus</i>, <i>Clarkina yini-Clarkina zhangi</i>, and <i>Hindeodus parvus</i> zones and the PTB is placed at approximately 12 m in the studied 19 m thick sequence. Three tuff layers in the lower part of Gua Panjang contain zircon grains with CA-TIMS U-Pb ages of 252.23 ± 0.07 Ma, 252.47 ± 0.12 Ma and 252.16 ± 0.16 Ma (maximum age), respectively. Conodont faunas from Gua Sei represent the Upper Permian (Changhsingian) <i>Clarkina hauschei - Hindeodus latidentatus</i> Zone and the basal Triassic lower Induan (Griesbachian) <i>Hindeodus parvus</i> and <i>Isarcicella staeschei</i> zones. The PTB is placed at 30 m above the base of the Gua Sei sequence.