The term refuge describes, in both ecology and paleoecology, an ecosystem that acts as a sanctuary during times of environmental stress. This study tests the concept by examining the fate of a single community that lived ∼50 k.y. after the end-Permian mass extinction (EPME). An assemblage of trace fossils, bivalves, and echinoids, living on a microbial mat in a slope environment, is preserved on a single bedding plane in the Shangsi section, south China. The microbial community was vital to the success of the refuge, acting as a stable substrate, food source, and oxygen supply. Shallow-water microbial communities have been interpreted as refugia, but this deeper site may have been critical to organisms with temperature sensitivities. Published paleotemperature calculations suggest sublethal surface temperatures of 34 °C at Shangsi. A species of cidaroid echinoid likely migrated to cooler deep waters to optimize development, suggesting that the success of this shallow-water clade is attributable to such refugia, when survival was most precarious after the EPME. The ecosystem was short lived, depending on low productivity and slow sedimentation. When conditions became suboptimal due to ash input and increasing productivity, the ecosystem quickly collapsed, allowing for colonization by opportunistic taxa including Claraia and microconchids. Elsewhere the ecosystem may have remained unchanged. Earliest Triassic refugia may have been restricted to these ephemeral environmental settings until organisms adapted to continuing harsh conditions.