During the American Civil War, Confederate soldiers under the command of General Robert E. Lee again mined the cave for nitre.

[4] Formerly, a famous fossil discovery—that of Thomas Jefferson's giant ground sloth (Megalonyx jeffersonii)—had been assumed to have come originally from Organ Cave.

In the early 20th century, a local man, Andrew Price of Marlinton, decided that the fossil had come from Organ Cave and popularized his theory.

[9] In 1995, however, Smithsonian paleontologist Frederick Grady proposed[10] that Haynes Cave in nearby Monroe County was the true source.

In 2008, the governor of West Virginia held a ceremony at Organ Cave to present the owner with a certificate stating that M. jeffersoni was the "Official West Virginia State Fossil" and repeated the assertion that it was indeed found in Organ Cave, but without producing any new evidence.