The anterior-posterior (A-P) axis of the vertebrate body plan is established during gastrulation, as mesoderm is progressively generated and patterned by signaling from the posterior midline through the node and primitive streak. In this thesis, I describe a novel role for midline Hedgehog (Hh) signaling in the patterning of mesoderm lineages across the A-P axis. Single-cell transcriptome analysis of Hh-deficient mesoderm revealed selective deficits in anterior mesoderm populations that later translate to physical defects to anterior embryonic structures including the first pharyngeal arch, heart, and anterior somites. I found that Hh-dependent anterior mesoderm defects were cell non-autonomous to Hh-signal reception. Transcriptional profiling of Hh-deficient mesoderm during gastrulation revealed disruptions to both transcriptional patterning of the mesoderm and a key FGF signaling pathway for mesoderm migration. Finally, cellular migration during gastrulation was decreased by Hh pathway antagonism and could be restored by addition of FGF4 protein. Together, my findings define a novel midline Hh-FGF signaling axis during gastrulation required for A-P embryonic patterning. Additionally, I observed a separate role for Hh signaling in the patterning of extraembryonic tissues involved in early blood formation. Hh-deficient mesoderm showed a severe downregulation of blood transcripts at E8.5 and an upregulation of endothelial genes. Sc-RNAseq confirmed that Hh mutants displayed sparse erythrocyte contribution and increased contribution to both hemogenic and non-hemogenic endothelium. Single-cell gene expression analysis revealed that Hh mutants showed proportional enrichment of hemogenic precursors that arise from both first and second wave hematopoiesis. This challenges the prevailing model which states that Hh mutations cause blood defects through a primary insufficiency of hemogenic precursor development from nascent mesoderm. Rather, Hh mutants form sufficient hemogenic precursors but later experience impaired ability to differentiate into functional erythrocytes.