The Blydefontein Rock Shelter is a Later Stone Age archaeological site in the eastern Karoo of South Africa. No remains of domesticated animals have been reported although a dung layer, interpreted as deriving from sheep, dates to approximately one thousand years ago. The published morphological analyses of the site’s fauna include many wild taxa, but also report that the majority of the bones in the assemblage were too fragmentary to identify. A recent re-examination of the assemblage identified ten specimens as examples of sheep or goats. In this paper we report on ancient DNA research on the eight specimens we were sent to study, six of which have preserved DNA. Of these, five are examples of wild animals, all of which had been previously identified as present at the site. One specimen was confirmed as a sheep, and it likely comes from a layer that dates to a period well after the initial introduction of domesticates. Direct dating of the specimen is not possible as the entire sample was consumed by the genetic testing. This study highlights the importance of ancient DNA as confirmation of taxon identification when the results of morphological identification challenge the broader culture history.