Xyliphius sofiae can be diagnosed from all its congeners by four autapomorphies: absence of eyes (vs. presence, though reduced); color pale, lack of pigment (vs. head and body darkly pigmented); 5 branchiostegal rays (vs. 4); and unculiferous tubercles on posterior body evenly distributed (vs. enlarged unculiferous tubercles typically arranged in five distinct rows from above pelvic-fin base to posterior end of caudal peduncle). It further differs by having one ossified proximal radial in the pectoral fin (vs. two in congeners, except X. magdalenae, not examined). It can be distinguished from all congeners except X. lepturusby having the snout tip elongated and narrowly rounded (vs. short and broadly rounded, often with small median notch), fifth ceratobranchial relatively narrow with two or three irregular rows of acicular teeth (vs. broadly expanded with larger conical teeth), anterior limits of the branchial apertures separated by a distance smaller 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) (Ref. 116022).