Marsupials display accelerated development of the craniofacial region relative to the differentiation of the CNS when compared to placental mammals. This heterochrony is thought to be due to the functional demands on the oral region for suckling post-birth while in a highly altricial state after a very short gestation period. While cis-regulatory regions are thought to play a significant role in morphological evolution of the mammalian face, the genetic mechanisms involved in craniofacial heterochrony in marsupials remain unclear. To assess this question, we generated ChIP-seq data for H3K4me3 and H3K27ac from fat-tailed dunnart (Sminthopsis crassicaudata; Dasyuridae) craniofacial tissue collected from pouch young on the day of birth and characterised the cis-regulatory landscape during craniofacial development. Using data from the mouse ENCODE consortium we explore the similarities and differences in active regulatory pathways between the dunnart and mouse during early craniofacial development. We found that dunnart promoter- and enhancer- associated peaks overlap to some extent with all the stages (E10.5 – E15.5) in the mouse. However, dunnart genes with peaks were significantly enriched for genes that exhibit linear increases in expression from E10.5 to E15.5 in mice, suggesting a greater similarity with late development. In turn, genes displaying this temporal expression pattern were enriched for Gene Ontology terms related to ossification and skeletal development, processes that underlie development of the cranial muscles and bones of the face. This study provides useful insights into genomic regions associated with cis-regulatory elements regulating craniofacial development in marsupials and their potential role in craniofacial heterochrony.