Xyliphius sofiae, new species, is described based on a unique specimen exhibiting four autapomorphies: eyes absent vs. present (though reduced); color pale, lacking pigment vs. head and body darkly pigmented; branchiostegal rays five vs. four; and unculiferous tubercles on posterior body distributed evenly vs. enlarged unculiferous tubercles typically arranged in five distinct rows above pelvic-fin base to posterior end of caudal peduncle. In addition, the pectoral fin of X. sofiae, new species, has one ossified proximal radial vs. two in congeners (except X. magdalenae, not examined). Xyliphius sofiae, new species, differs from all congeners except X. lepturus by snout tip elongated and narrowly rounded vs. short and broadly rounded, often with small median notch; fifth ceratobranchial relatively narrow with elongate acicular teeth vs. broadly expanded, leaf-shaped, with shorter and broader, conical teeth; anterior limits of branchial apertures separated by distance less than length of aperture vs. greater than length of aperture; anal-fin rays modally nine vs. seven; and lateral line extending onto base of caudal-fin rays vs. finishing in hypural region. Based on the single specimen collected in the main channel of the Río Amazonas near Iquitos, Peru, we describe the osteology of X. sofiae, new species, using a non-invasive technique: high-resolution X-ray computed tomography (HRXCT). We consider Xyliphius lombarderoi Risso and Risso, 1964, a species based on a unique holotype that is now lost, to be a subjective junior synonym of X. barbatus Alonso de Arámburu and Arámburu, 1962. Variable characteristics are summarized for the seven species of Xyliphius treated here as valid, and their distributions are plotted based on a comprehensive review of museum specimens.