The anatomy and affinities of Jamoytius kerwoodi White have long been controversial, because its complex taphonomy makes unequivocal interpretation impossible with the methodology used in previous studies. Topological analysis, model reconstruction and elemental analysis, followed by anatomical interpretation, allow features to be identified more rigorously and support the hypothesis that Jamoytius is a jawless vertebrate. The preserved features of Jamoytius include W-shaped phosphatic scales, 10 or more pairs of branchial openings, optic capsules, a circular, subterminal mouth and a single terminal nasal opening. Interpretations of paired ‘appendages’ remain equivocal. Phylogenetic analysis places Jamoytius and Euphanerops together (Jamoytiiformes), as stem-gnathostomes rather than lamprey related or sister taxon to Anaspida.