Developmental regulatory networks constitute all the interconnections among molecular components that guide embryonic development. Developmental transcriptional regulatory networks (TRNs) are circuits of transcription factors and cis-acting DNA elements that control expression of downstream regulatory and effector genes. Developmental networks comprise functional subnetworks that are deployed sequentially in requisite spatiotemporal patterns. Here, we discuss integrative genomics approaches for elucidating TRNs, with an emphasis on those involved in Drosophila mesoderm development and mammalian embryonic stem cell maintenance and differentiation. As examples of regulatory subnetworks, we consider the transcriptional and signaling regulation of genes that interact to control cell morphology and migration. Finally, we describe integrative experimental and computational strategies for defining the entirety of molecular interactions underlying developmental regulatory networks.