Although Calligenethlon watsoni, an enigmatic embolomere from Joggins, Nova Scotia, has been known since 1934, an in-depth description of its anatomy and taxonomic diagnosis is missing from the literature, resulting in subsequent specimen referrals to be based largely on the nondiagnostic trait of small body size. Here, an exquisitely preserved Calligenethlon specimen is described in detail using micro-computed tomography. The anatomical knowledge gained here allowed for the re-evaluation of all referred specimens and creation of the first ever morphological diagnosis of Calligenethlon. This anatomical data was then used to test the prevailing hypothesis that braincase characters unite embolomeres in a stem tetrapod position. A series of analyses, using the most up-to-date sampling of characters and relevant tetrapod taxa, resulted in the conclusion that embolomeres do group together in a stem tetrapod position, but braincase characters are seemingly uninfluential in this placement, and taxon sampling may be of greater significance.