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Abstract Background The phylogenetic relationships of fossil birds near the origin of the avian crown group remain debated, in part due to a limited amount of character evidence from incomplete fossils. The avian lower jaw provides a potentially rich source of additional character data, yet fusion of the individual bony elements composing the avian post-dentary complex has impeded efforts to explore its phylogenetic signal. Here, we use high-resolution µCT-scanning to separate the individual bony elements of the mandibles of several immature crown birds and key fossil taxa, and use those data to assess support for alternative phylogenetic hypotheses for fossils near the origin of crown birds. Results We find that evidence from Asteriornis fails to support interpretations of derived mandibular similarities with palaeognaths, and instead strongly favours galloanseran, and specifically galliform, affinities. Our results also illustrate striking similarities in the architecture of the lower jaws between the toothed ornithurine Ichthyornis, Pelagornithidae and Vegavis, which, in addition to the absence of derived features linking them to Galloanserae, highlights questions regarding the phylogenetic position of these perennially controversial taxa. Conclusions Our data reveal new insight into patterns of morphological evolution near the origin of the avian crown group while raising new phylogenetic questions, emphasising the potential untapped value of detailed comparative investigations of morphological complexes such as the post-dentary complex of the mandible for informing the early evolutionary history of crown birds.