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Background  Runt-related transcription factor 2 ( RUNX2 ) is a transcription factor essential for skeletal development. Variation within the  RUNX2  polyglutamine / polyalanine (QA) repeat is correlated with facial length within orders of placental mammals and is suggested to be a major driver of craniofacial diversity. However, it is not known if this correlation exists outside of the placental mammals.    Results  Here we examined the correlation between the RUNX2 QA repeat ratio and facial length in the naturally evolving sister group to the placental mammals, the marsupials. Marsupials have a diverse range of facial lengths similar to that seen in placental mammals. Despite their diversity there was almost no variation seen in the RUNX2 QA repeat across individuals spanning the entire marsupial infraclass. The extreme conservation of the marsupial RUNX2 QA repeat indicates it is under strong purifying selection. Despite this, we observed an unexpectedly high level of repeat purity.    Conclusions  Unlike within orders of placental mammals,  RUNX2  repeat variation cannot drive craniofacial diversity in marsupials. We propose conservation of the marsupial RUNX2 QA repeat is driven by the constraint of accelerated ossification of the anterior skeleton to facilitate life in the pouch. Thus, marsupials must utilize alternate pathways to placental mammals to drive craniofacial evolution.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-017-0955-6) contains supplementary material, which is available to authorized users.

RUNX2 repeat variation does not drive craniofacial diversity in marsupials