The U.S. Geological Survey St. Petersburg Coastal and Marine Science Center’s (USGS SPCMSC) Core Archive in St. Petersburg, FL contains a collection of coral-reef cores collected from throughout the Florida Keys reef tract (FKRT). In a previous study (Toth and Stathakopoulos, 2019), USGS researchers analyzed the upper, Holocene (~11,700 years ago to present) sections of those cores to evaluate how the coral composition of the FKRT changed over millennial timescales. Using the same methods, USGS researchers quantified the relative composition of late Pleistocene (~116 to 74 thousand years before present; Marine Isotope Stages [MIS] 5d, 5c, 5b, and 5a) sections of the coral reef cores dated by Hsia and others (2024a,b). This data release provides metadata about the location of the cores and summarizes the relative composition of coral taxa and other carbonates and the water depths (relative to modern mean sea level) of the analyzed core intervals. The data release also provides a summary of previously unpublished data (collected by David Weinstein) on the relative composition of an older Late Pleistocene reef (growing ~130–116 thousand years before present; MIS5e) from the subaerially exposed fossil reef at Windley Key Fossil Reef Geological Park. These data are compared with Holocene and modern coral-reef assemblages on the FKRT in Toth and others (2025).