In the emerging discipline of Evo-Devo, the analysis of gene expression patterns can be deceptive without a clear understanding of the underlying regulatory strategies. Here, we use the paradigm of hand and foot evolution to argue that the consideration of the regulatory mechanisms controlling developmental gene expression is essential to resolve comparative conundrums. In this context, we discuss the adaptive relevance of evolving stepwise, distinct developmental regulatory mechanisms to build an arm, i.e., a composite structure with functional coherence.