Organic carbon (OC) burial is an important process influencing atmospheric CO2 concentration and global climate change; therefore it is essential to obtain information on the factors determining its preservation. The Southern Ocean (SO) is believed to play an important role in sequestering CO2 from the atmosphere via burial of OC. Here we investigate the degradation of organic-walled dinoflagellate cysts (dinocysts) in two short cores from the SO to obtain information on the factors influencing OC preservation. On the basis of the calculated degradation index kt, we conclude that both cores are affected by species-selective aerobic degradation of dinocysts. Further, we calculate a degradation constant k using oxygen exposure time derived from the ages of our cores. The constant k displays a strong relationship with pore-water O2, suggesting that decomposition of OC is dependent on both the bottom- and pore-water O2 concentrations.