New data have been obtained on major- and trace-element compositions and Sm–Nd isotope systematics of clastic metasediments that belong to the Kornilova and Shubutui Formations in the Khamar-Daban terrane. The Kornilova Formation flysch derived from felsic mature crust, while the Shubutui Formation, with 4.5–7.5 wt.% MgO and higher Cr and Ni contents, had a mafic–ultramafic protolith of an island-arc setting. Isotope data indicate significant inputs of Precambrian crustal material (εNd(T) = –10 to –6.2) to the protolith of the Kornilova rocks and of high amounts of synsedimentary juvenile material to the protolith of the Shubutui Formation (εNd(T) = –2.9 to –1.5). Different model ages (1.7–2.0 and 1.3–1.4 Ga, respectively), compositions, and provenances of the Kornilova and Shubutui rocks, as well as a prolonged deposition gap (>100 Myr), evidence that the two formations were deposited in different basins and tectonic settings. The rock compositions and Nd isotope signatures suggest an island arc setting for the Shubutui deposition in the Dzhida terrane and a continental-margin setting for the deposition of the Kornilova Formation, which is the uppermost straton of the Khamar-Daban terrane.