The diversity and last appearance patterns of different taxa, inhabiting varied palaeo-water depths, can provide significant insights into the deterioration process of palaeoecosystems. This paper systematically summarizes the last appearance of the end-Permian planktons (including deep-water, intermediate-water, and shallow-water radiolarians) and benthos (including ostracods, foraminifers, brachiopods and bivalves) from Dongpan, a deep-water section of South China. Results show that the deep-water radiolarian Albaillellaria was the first order to go extinct, quickly followed by the intermediate- and shallow-water radiolarians and bottom-water ostracods and foraminifers. This was followed by the extinction of the bottom-water brachiopods and bivalves. We propose that the two-stage extinction pattern was related to the end-Permian migration and vertical expansion (both upward and downward) of an oxygen minimum zone (OMZ) along the southern margin of South China.