The cellular complexity and scale of the early liver have constrained analyses examining its emergence during organogenesis. To circumvent these issues, we analyzed 45,334 single-cell transcriptomes from embryonic day (E)7.5, when endoderm progenitors are specified, to E10.5 liver, when liver parenchymal and non-parenchymal cell lineages emerge. Our data detail divergence of vascular and sinusoidal endothelia, including a distinct transcriptional profile for sinusoidal endothelial specification by E8.75. We characterize two distinct mesothelial cell types as well as early hepatic stellate cells and reveal distinct spatiotemporal distributions for these populations. We capture transcriptional profiles for hepatoblast specification and migration, including the emergence of a hepatomesenchymal cell type and evidence for hepatoblast collective cell migration. Further, we identify cell-cell interactions during the organization of the primitive sinusoid. This study provides a comprehensive atlas of liver lineage establishment from the endoderm and mesoderm through to the organization of the primitive sinusoid at single-cell resolution. Display omitted •Single-cell analyses provide a comprehensive atlas of liver cell lineage emergence•A distinct, migratory, hepatomesenchymal hybrid cell type is identified•Liver endothelial and mesenchymal progenitors emerge during early hepatogenesis•Candidate cell-cell interactions are identified within the primitive liver sinusoid A comprehensive atlas of mouse liver emergence is described at single-cell resolution starting at endoderm progenitor specification, including data detailing divergence of vascular and sinusoidal endothelia, hepatoblast specification, and the emergence of a distinct, migratory hepatomesenchymal cell type.