The South China Sea (SCS) is situated at the junction of the Eurasian, Pacific, and Indo-Australian plates. It has undergone nearly a complete Wilson cycle despite its relatively small size and short evolutionary history, and it is a critical site linking some of the major western Pacific tectonic units. The opening of the SCS reveals complex patterns of continental margin breakup and basin formation. Despite extensive studies, sampling of basement rocks and overlying sediments in the deep basin is currently lacking. This leaves a large margin of error in estimated opening ages and renders various hypotheses regarding its opening mechanism and history untested. This also hampers our understanding of East Asian tectonic and paleoenvironmental evolution. International Ocean Discovery Program Expedition 349 (28 January–30 March 2014) will drill three sites to ~100 m into basement (Sites SCS-3G, SCS-6A, and SCS-4B) in two different sub-basins of the SCS to address questions regarding the opening and evolution of the SCS and how it affected the paleoceanography of the region. These sites are located to determine the timing of onset and cessation of seafloor spreading in the East and Southwest Sub-basins. Geochemical sampling of basement rocks of different ages within the different magnetic zones of the SCS will provide critical information on how the crust and mantle evolved during various stages of basin evolution. Coring of the sedimentary section above basement will provide direct constraints on the age of the underlying basement through biostratigraphy and will allow examination of changes in sedimentation and paleoceanography through time as the basin opened and then began subducting beneath the Manila Trench. All sites will be single cored using the advanced piston corer and extended core barrel to refusal, followed by rotary core barrel drilling through the remaining sediment section and basement. If permitted by the Environmental Protection and Safety Panel, we will drill through the top 900 m of the highest priority site (SCS-6A), which would recover a similar sequence to that cored at the first site (SCS-3G). This option gives the best opportunity of reaching and coring basement at all three primary sites. If full coring is required, two additional sites that reach basement with shallower penetration will be substituted. Downhole logging is planned for all sites using the triple combination and Formation MicroScanner–sonic tool strings. Additional tool strings may be run if time and hole conditions permit, including a check shot survey, the Ultrasonic Borehole Imager, the magnetometer tool, and the magnetic susceptibility sonde.