Previous work has revealed that Hippopotamyrus ansorgii (Boulenger, 1905) is a species complex, with specimens from the Upper Zambezi system (Caprivi Strip in Namibia) that are well differentiated from the Angolan type specimens. Here, we sampled the Cunene River, one of several possible type rivers for H. ansorgii, on the border between Namibia and Angola. The specimens are morphologically differentiated from the six other known morphs within the H. ansorgii species complex, including the types and H. szaboi. The electric organ discharge of the Cunene specimens has a different pulse waveform and associated amplitude spectra to that of the three Upper Zambezi system morphs of the species complex. The Cunene specimens are genetically distinct, but relatively closely related to other taxa of the H. ansorgii complex, such as the Upper Zambezi system morphs. We recognize the Lower Cunene morph as the new species, Hippopotamyrus longilateralis sp. nov.