Salamander phylogeny has been difficult to assess via morphology due to paedomorphosis, the retention of juvenile characters in the adult form, resulting in a large discrepancy between the topologies recovered by morphological and molecular datasets, prompting one author to comment that ontogeny “discombobulates” phylogeny. To investigate whether the addition of braincase morphology, an evolutionarily conserved module, to the current character set can resolve the incongruence between morphological and molecular datasets, I scanned 28 specimens of salamander, representing all 10 families, with micro-computed tomography; this represents the first time all 10 families have been visualized in 3D. I created a set of morphological characters describing the braincase, which I concatenated with the current datasets and performed both parsimony and Bayesian analyses. My results suggest that metamorphosis is strongly misleading morphological topologies, and demonstrate the importance of understanding how development impacts terminal morphology for character selection in future phylogenetic analyses.