Cleft palate is a common craniofacial disorder involving multiple genetic and environmental predisposing factors. Currently, limited insight exists into the molecular mechanisms regulating osteogenic differentiation and patterning in the palate during embryogenesis. This study utilized thePax9-deficient mouse genetic model of cleft palate to investigate the role ofPax9in osteogenic differentiation. Single-nucleus transcriptomics and chromatin accessibility assays validated by whole-transcriptome and single-molecule spatial transcriptomics suggest a relationship between separatePax9+ and osteogenic populations. Loss ofPax9resulted in premature osteogenic differentiation and bone maturation. The spatially restricted osteogenic domains inPax9−/−mice are bounded byDkk2, which normally interfaces withPax9in the mesenchyme. Together, these results confirm a regulatory role for the Wnt pathway in patterning of palatal bone, offering novel insights into the complex nature of developmental signaling and osteodifferentiation in the palate.