Significance The vertebral column provides essential structural and protective functions. The total number of vertebral elements and their specific morphologies are remarkably reproducible within a given species, yet can be tailored to the requirements of separate vertebrate species. Major genetic determinants driving formation of the vertebral column are known, but how they are regulated to achieve a highly reproducible structure remains to be fully elucidated. In this report, we show that the miR-196 family of microRNAs are essential in defining correct vertebral number and vertebral identity in mouse. We reveal the molecular landscape controlled, either directly or indirectly, by miR-196 activity, to demonstrate that miR-196 impacts many key developmental signalling pathways and reinforces a timely trunk-to-tail Hox code transition.