Rupert Cave has never had a large bat population, although four bat species have been found in the cave; Northern Long Eared, Eastern Pipistrelle, Big Brown and Little Brown bats. In 2001 a bat gate was added to the side of the entrance building. Over the following eight years the bat count would climb from 25 to 150. In 2009 White Nose Syndrome was found in nearby Mifflin County caves and in 2010 WNS was discovered in Rupert. In February 2011 the bat count had dropped to 62. Long tailed and slimy salamanders can frequently be found near the cave entrance during the summer months. In 1999 a small puddle in the Ballroom was found to contain baby salamanders. Five-lined skinks are also sighted outside of the cave building during the summer. According to different articles and findings, bones from a pheasant, sheep, dogs, bats, and mice have been found in the cave. Snakes’ skins have been seen in the cave, actually in a mouse nest. And one report tells of finding bear hair in mud balls far into the cave.