During cardiogenesis in the mouse, the second heart field (SHF) is the source of the myocardium of the outflow tract and it contributes to other regions of the heart with the exception of the primitive left ventricle. This contribution corresponds with that of the second myocardial cell lineage, identified by retrospective clonal analysis. Gene regulatory networks, signaling pathways, and heterogeneity within the SHF are discussed, together with the question of regulation of myocardial progenitor cells within the first heart field. The extension of the SHF into the mesodermal core of the arches also gives rise to endothelial cells of the pharyngeal arch arteries. Knowledge about the origin and genetic regulation of cells that contribute to the heart and associated vasculature is important for the diagnosis and treatment of congenital heart malformations.