AbstractHigh levels of morphological homoplasy have hindered progress in understanding morphological evolution within gymnophione lissamphibians. Stemming from the hypothesis that the braincase has the potential to yield phylogenetic information, the braincases of 27 species (23 genera) of gymnophione amphibians were examined using high‐resolution micro‐computed tomography and histologically prepared specimens. Morphology of the brain and its relationship to features of the braincase is described, and it is shown that eight different patterns exist in the distribution of foramina in the antotic region. The distribution of variants is congruent with molecule‐based phylogeny. Additionally, all variants are shown to correspond directly to stages along developmental continua, suggesting that the evolutionary truncation of development in the antotic region at various stages has driven the evolution of morphology in this region. Attempts to correlate the observed morphology with proxies of putative heterochronic events (including those attributable to burrowing, life history, and size) fail to explain the distribution of morphology if each proxy is considered separately. Thus, it is concluded that either currently unrecognized causes of heterochrony or combinations thereof have influenced morphology in different lineages independently. These data identify clades whose morphology can now be reconsidered in light of previously unrecognized heterochronic events, thereby providing a foundation for future analyses of the evolution of morphology within Gymnophiona as a whole. Most significantly, these data confirm, for the first time in a lissamphibian group, that the braincase can preserve important phylogenetic information that is otherwise obscured in regions of the skull that experience strong influences from functional constraints. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc.