The offshore Cuu Long (CLB) and Nam Con Son (NCSB) basins of SE Vietnam are two important Cenozoic hydrocarbon-bearing basins in the southern South China Sea (SCS), which can contribute to understanding the evolution of major SE Asian river systems, in particular the Mekong River. The Oligocene to Early Miocene basin fill of the Cuu Long Basin is dominated by sediment sourced locally from the Da Lat Zone basement on land. Sandstones have abundant Cretaceous detrital zircons and heavy mineral assemblages dominated by apatite and epidote. The Bach Ho Unconformity at c. 16 to 20.5 Ma marks a major provenance change and the overlying Middle to Late Miocene Con Son and Dong Nai formations were sourced by a large river system, which drained Indochina or even the Himalaya, resembling the present-day Mekong River. These formations have heterogeneous detrital zircon populations dominated by Triassic ages and zircon–rutile–tourmaline-dominated heavy mineral assemblages. The Oligocene Cau and Early Miocene Dua formations of the Nam Con Son Basin have a similar provenance to the CLB Con Son and Dong Nai formations, indicating a comparable drainage history of a large proto-Chao Phraya. At the Dua Unconformity at c. 15.4 to 17 Ma the Indochina provenance signature changes to a predominant Sibumasu signature.The early Mekong River evolution is suggested to have involved two river systems. A proto-Mekong 1 initially filled the CLB, while at the same time a proto-Chao Phraya River with a capture area into the Himalaya filled the Malay Basin and/or the NCSB. At the end of the Early Miocene drainage was completely reorganised, and the proto-Mekong 1 captured the headwaters of the proto-Chao Phraya and became the proto-Mekong 2, while the NCSB was filled by sediment from the Malay–Thai Peninsula. This major change marks a very important drainage reorganisation in the southern SCS region.