A comprehensive single-cell RNA sequencing study of the mouse nervous system reveals a detailed molecular taxonomy of cell types, including seven distinct astrocyte types with regionally restricted distributions. The study maps cell types spatially and identifies a hierarchical, data-driven classification. Neurons, the most diverse cell type, are grouped by developmental anatomical units and neurotransmitter expression. Neuronal diversity is driven by genes related to cell identity, synaptic connectivity, neurotransmission, and membrane conductance. Astrocytes show regional specialization, correlating with the spatial distribution of key neurotransmitters. Oligodendrocytes lose regional identity and undergo secondary diversification. The study provides a reference atlas for understanding the mammalian nervous system, enabling genetic manipulation of specific cell types. The research highlights the molecular diversity of the nervous system, with distinct cell types in different regions, and shows that cell identity is influenced by developmental ancestry, local environment, and function. The study also identifies the molecular diversity of astrocytes, ependymal cells, and radial glia, and reveals the convergence of oligodendrocyte lineage to a common state. The study further describes the diversity of vascular cells and neural-crest-like glia, and identifies distinct cell types in the peripheral and central nervous systems. The findings provide a detailed molecular map of the mouse nervous system, revealing the complex organization and diversity of cell types.A comprehensive single-cell RNA sequencing study of the mouse nervous system reveals a detailed molecular taxonomy of cell types, including seven distinct astrocyte types with regionally restricted distributions. The study maps cell types spatially and identifies a hierarchical, data-driven classification. Neurons, the most diverse cell type, are grouped by developmental anatomical units and neurotransmitter expression. Neuronal diversity is driven by genes related to cell identity, synaptic connectivity, neurotransmission, and membrane conductance. Astrocytes show regional specialization, correlating with the spatial distribution of key neurotransmitters. Oligodendrocytes lose regional identity and undergo secondary diversification. The study provides a reference atlas for understanding the mammalian nervous system, enabling genetic manipulation of specific cell types. The research highlights the molecular diversity of the nervous system, with distinct cell types in different regions, and shows that cell identity is influenced by developmental ancestry, local environment, and function. The study also identifies the molecular diversity of astrocytes, ependymal cells, and radial glia, and reveals the convergence of oligodendrocyte lineage to a common state. The study further describes the diversity of vascular cells and neural-crest-like glia, and identifies distinct cell types in the peripheral and central nervous systems. The findings provide a detailed molecular map of the mouse nervous system, revealing the complex organization and diversity of cell types.