Our multidisciplinary study of historic Thoroughbred horses solves two long-running mysteries in racing history. Eclipse, the greatest racehorse ever known, never lost a race. His skeleton is housed in the Royal Veterinary College, London; however, there is controversy over its authenticity. The 1880 Epsom Derby was won by Bend Or. In one of the great controversies of Thoroughbred racing, the owners of Bend Or were accused of swapping him with another horse, Tadcaster, whose maternal pedigree was more prestigious. Bend Or's skeleton resides at the Natural History Museum, in London. Eclipse and Tadcaster were both extremely popular at stud, and the vast majority of racehorses today are descendents. We compared mitochondrial DNA haplotypes of living and historic Thoroughbred skeletons, including those of Eclipse and Bend Or. Additionally, we compared skeletal morphometrics of Eclipse's skeleton with measurements taken at autopsy. Carbon and nitrogen stable isotopes of a range of skeletal elements were compared in order to establish that the Eclipse skeleton was that of a single horse. Our multidisciplinary data suggest that the putative skeleton is consistent with that of Eclipse. In contrast, mitochondrial DNA haplotype sharing indicated that the skeleton known as Bend Or is most probably that of Tadcaster.