Past variations in the strength of the Atlantic meridional overturning circulation (AMOC) triggered large and rapid climate changes at hemispheric and global scales for at least the last 90,000 years, raising the question: how have these millennial-scale climate oscillations affected contemporary biodiversity? Here we examine legacies of millennial-scale climate oscillations on contemporary species richness in eastern North America. We analyze a combination of 13 palaeoclimate estimates from proxy-based reconstructions, hosing-only climate simulations, and transient simulations of the last deglaciation, as predictor variables in spatial error models (SEM) explaining contemporary richness for amphibians, passerine birds, mammals, reptiles, and trees. Results suggest that past climate changes due to AMOC variations have left imprints on the contemporary richness of mammals, and some on trees. In particular, high temperature stability, precipitation increase, and an apparent climate fulcrum in the southeastern United States across millennial-scale climate oscillations is predictive of greater contemporary richness, suggesting a mechanism for why this region was a possible climatic refuge. However, the strength and direction of palaeoclimate-richness relationships varies among SEMs fit to different palaeoclimate estimates, pointing to the importance of palaeoclimatic ensembles and the need for caution when basing biogeographic interpretations on individual palaeoclimate simulations.