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Background Macelognathus vagans Marsh, 1884 from the Late Jurassic Morrison Fm. of Wyoming was originally described as a dinosaur by Marsh and in 1971 Ostrom suggested crocodilian affinities. In 2005, Göhlich and collaborators identified new material of this species from Colorado as a basal crocodylomorph. However, a partial skull found in association with mandibular and postcranial remains was not described. Methods Due to the small size and delicate structures within the braincase, micro CT studies were performed on this specimen. The new anatomical information was incorporated in a phylogenetic dataset, expanding both character and taxon sampling. Results This new material reinforces the non-crocodyliform crocodylomorph affinities of Macelognathus as it bears a large otic aperture, unfused frontals and lacks ornamentation on the dorsal cranial bones. The internal structures also support these affinities as this specimen bears traits (i.e., heavily pneumatized and expanded basisphenoid; the presence of additional pneumatic features on the braincase; and the otoccipital-quadrate contact) not present in most basal crocodylomorphs. Furthermore, the presence of a wide supraoccipital and a cranioquadrate passage are traits shared with Almadasuchus from the early Late Jurassic of Argentina. Macelognathus was recovered as one of the closest relatives of crocodyliforms, forming a clade (Hallopodidae) with two other Late Jurassic taxa ( Almadasuchus and Hallopus ). Discussion The clade formed by Almadasuchus + Hallopus + Macelognathus , the Hallopodidae, is characterized by a higher degree of suturing of the braincase, posteriorly closed otic aperture (paralleled in mesoeucrocodylians) and cursorial adaptations. Also, the phylogenetic position of this lineage of derived crocodylomorphs as the sister group of Crocodyliformes implies a large amount of unsampled record (ghost lineage), at least 50 million years.