Little is known regarding the internal anatomy of thelodonts, with most of the available information coming from a single specimen, the holotype of Turinia pagei (Powrie). Previous descriptions have led to many partial, or conflicting interpretations. Herein, we describe fully the anatomy of T. pagei based on the holotype and additional material. T. pagei possessed a branchial system composed of eight pairs of gills, a buccal/nasohypophyseal region lined with minute denticles, comparable to buccopharyngeal denticles of sharks, and possessed a stomach which is preserved by sediment infill in the holotype specimen. Contrast between the petrological character of the gut infill and the sediment in which the animal is preserved suggests that the gut was infilled in vivo and that T. pagei was probably a deposit feeder. Phylogenetic analysis resolves T. pagei and the Galeaspida as sister-taxa, comprising a sister-group to the Osteostraci plus jawed vertebrates. In contrast to the view that has prevailed hitherto, thelodonts with a dorsoventrally compressed cross-sectional profile comprise a monophyletic group, of which T. pagei is the least derived member. The furcacaudiforms are resolved as an unnatural group, one taxon being the sister taxon to the ‘conventional’ thelodont clade, and the other, the sister taxon to this clade plus galeaspids, osteostracans and jawed vertebrates. The analysis agrees with the earlier view that thelodonts lack distinct synapomorphies, but we argue that distinct synapomorphies are not a requisite of monophyly.