Ages of corals and shallow-marine sequences define rates of marine invertebrate evolution, tectonic uplift, and paleoclimate change, yet accurate ages are difficult to obtain prior to the late Pleistocene. We report a new approach for combining uranium-lead (U- Pb) and uranium-series dating for middle Pleistocene corals from the Caribbean side of Costa Rica. Two corals have 230Th/238U in secular equilibrium, small excesses in δ234U, and 206Pb*/238U ages of 1.02 ± 0.07 Ma and 1.288 ± 0.034 Ma. The latter coral age dates a recognized geomagnetic event to ca. 1.3 Ma, a time at which no polarity events had been identified. The new ages also show that the major coral extinction in the Caribbean Basin occurred shortly after 1.0–0.9 Ma, much more recently than previously thought. This coral extinction now coincides with the global change at 1.0–0.8 Ma to the current pattern of glacial-interglacial cycles and amplified changes in sea level. These factors may have provided a new, strong environmental mechanism for rapid habitat modification and coral extinction.