Fossil cold-water corals can be used to reconstruct physical, chemical, and biological changes in the ocean because their skeleton often preserves ambient seawater signatures. Furthermore, patterns in the geographic and temporal extent of cold-water corals have changed through time in response to environmental conditions. Here we present taxonomic and dating results from a new collection of subfossil cold-water corals recovered from seamounts of the Southwest Indian Ocean Ridge. The area is a dynamic hydrographic region characterised by eastward flow of the Agulhas Return Current and the northernmost fronts of the Antarctic Circumpolar Current. In total, 122 solitary scleractinian corals and 27 samples of colonial scleractinian material were collected from water depths between 172 and 1395 m, corresponding to subtropical waters, Antarctic Intermediate Water (AAIW), and Upper Circumpolar Deep Water (UCDW). Fifteen species were identified, including eight species new to the region. The assemblage reflects the position of the seamounts in a transition zone between Indo-Pacific and Subantarctic biogeographic zones. Morphological variation in caryophyllids and the restriction of dendrophylliids to the southern seamounts could result from genetic isolation or reflect environmental conditions. Uranium-series dating using both rapid laser ablation and precise isotope dilution methods reveals their temporal distribution from the Last Glacial Maximum to the present day. Only one specimen of glacial age was found, while peaks in abundance occur around Heinrich Stadial 1 and the Younger Dryas, times at which ocean chemistry and food supply were likely to have presented optimal conditions for cold-water corals. A widespread regional preference of cold-water corals for UCDW over AAIW depths during the deglacial, the reverse of the modern situation, could be explained by higher dissolved oxygen concentrations and a temperature inversion that persisted into the early Holocene.