The pimelodid catfish genus Hypophthalmus has an unusually modified Weberian apparatus, reduced swim bladder, and associated bones of the occiput and pectoral girdle. Using high resolution X-ray tomography and traditional skeletal preparations of adult and juvenile specimens, we reexamined and illustrated this occipito-vertebral complex. Comparisons were made to the plesiomorphic architecture of the complex exhibited by phylogenetically deep pimelodid genera. Hypophthalmus has the swim bladder reduced to a pair of separate bilobed sacs, each doubly encapsulated by outer and inner layers of bone. The anterior vertebrae and occipital bones are shortened and contorted with apparent loss or fusion of the first centrum and development of novel joints between the basioccipital and complex vertebra. Two pairs of the Weberian ossicles are lost: claustra and intercalaria. The posttemporal-supracleithrum is reshaped and solidly united to a recurved arm of the 4^th parapophysis with both extended far posteriorly to brace the outer swim bladder capsule and articulate with the cleithrum. The extrascapula is found in juveniles and apparently fuses with the adjacent pterotic. The third supraneural is present between the supraoccipital and complex vertebra. We point out conflicting results and interpretations among four previous studies and our treatment of the occipito-vertebral complex and swim bladder of Hypophthalmus. Based on unambiguous morphological and molecular evidence, Hypophthalmus belongs to the sorubimine clade of the family Pimelodidae. In this evolutionary context the morphology of the occipito-vertebral complex and swim bladder of Hypophthalmus is distinctly divergent from that of other sorubimines. The complex of Hypophthalmus is also distinct from the partially encapsulated swim bladders of the Calophysus and Megalonema clades. The morphology of the occipito-vertebral complex and swim bladder of Hypophthalmus is uniquely autapomorphic.