A core issue in evolutionary biology is if convergent fluctuations in proteins or regions drive convergent phenotypic development. We combined phylogenomic, developmental, and epigenomic analysis of 11 fresh genomes of paleognathous birds, including an extinct moa, to demonstrate that convergent evolution of regulatory areas, more than protein-coding genes, is widespread among developmental pathways connected with independent losses of flight. A Bayesian analysis of noncoding elements, 60,665 of which can be corroborated by open chromatin countries throughout development, identified 2355 separate accelerations for driving gene expression in the developing forelimb with functional consequences, along lineages of flightless paleognaths. Our results imply that the landscape associated with convergence in ratites includes a substantial component that is shared.