Evidence from stratigraphic sections of the Panthalassa, Paleo-Tethys and Neo-Tethys suggests that the oceans experienced widespread anoxia during the Late Permian, which likely contributed to the extinction of ~90% of marine and ~70% of terrestrial species. The Late Permian and Early Triassic were also characterized by significant carbon isotope excursions implying that considerable perturbations in the carbon cycle occurred. Bathymetric features of the Panthalassa during this period are not well known since most of the ocean floor has been subducted; however, tectonic reconstructions suggest that active marine subduction zones surrounded Pangea. Thus, it is reasonable to assume that there was an active mid-ocean ridge system located in Panthalassa during the Late Permian. In this study, the impact of such a spreading center within Panthalassa on the climate and carbon cycle is investigated using a comprehensive climate system model for the end-Permian. This is a novel approach because a majority of previous simulations assumed a flat bottom for the Panthalassa deep-sea. The mid-ocean ridge (MOR) simulation enhanced vertical mixing and topographic steering of the currents near the ridge-axis but in comparison with the simulation using a flat bottom, changes in the global distribution of water masses and circulation in the Panthalassa were insignificant. Dissolved oxygen concentrations were not considerably affected by the implementation of the mid-ocean ridge. Thus the approximation of using a flat-bottom topography in ocean models for the Late Permian remains valid.In a second sensitivity study, the effect of a sill between the deep Paleo-Tethys and Panthalassa on water mass distribution and oxygen content has been investigated. Model results suggest that the introduction of a sill led to enhanced stratification, as well as an increase in salinity and temperature in the Paleo-Tethys. An associated reduction of the dissolved oxygen concentration to dysoxic to near-anoxic conditions below 1800m suggests that the changes in sill height between the Paleo-Tethys and Panthalassa may have been a contributing factor of regional importance to the Permian-Triassic mass extinction.