Polypterid fishes are considered the basal-most group of extant actinopterygians and may be a direct link to understanding the systematics and evolution of the first bony fishes. Several investigations have been conducted on one member genus, Polypterus; however, since the first specimens of its sister taxon Erpetoichthys calabaricus were described, remarkably little work has been done on the species. We review terminology critical to understanding cranial morphology in polypterids and present a new description of the skull of E. calabaricus as observed through classical methods of skeletal preparation, X-radiographic microfocus computed tomography, and 3D-digital reconstruction. Differences among E. calabaricus and at least three species of Polypterus (P. bichir, P. senegalus, and P. endlicheri), besides the gross variation in size, include an overall elongation of the skull roof observable in most elements of E. calabaricus with a shortening of most associated processes. In addition, several elements present in species of Polypterus are absent in E. calabaricus. As a result, Polypterus should not be used as a proxy for the family Polypteridae to the exclusion of E. calabaricus in phylogenetic studies, which examine early actinopterygians. Each should be treated separately, to resolve inter- and intrarelationships of Polypteridae. © 2007 Wiley-Liss, Inc.