A multiomic consensus atlas of 1.8 million nuclei across human, macaque, and marmoset basal ganglia defines 61 conserved cell types and reveals that dorsal-ventral spatial patterning is more evolutionarily constrained than direct-indirect pathway or striosome-matrix molecular identity, while conserved transcription factor motif grammars specify cell type-specific enhancer activity and psychiatric disease risk is preferentially enriched in ventral striatal medium spiny neuron populations.

The basal ganglia (BG) are conserved brain regions essential for motor control, learning, emotion, and cognition, and are implicated in neurological and psychiatric disease. Yet a unified cross-species taxonomy of BG cell types is lacking, limiting translation of BG circuit mechanisms, interpretation of human genetic risk, and development of cell type-targeted tools. We present a multiomic consensus atlas of 1.8 million nuclei from human, macaque, and marmoset spanning eight BG structures. Integrating cross-species gene expression, open chromatin, and spatial profiling enables definition of conserved and divergent cell types. Alignment to existing mouse and human atlases identifies 61 homologous cell types conserved over 80 million years. We identify a STRd D2 StrioMat Hybrid medium spiny neuron (MSN) type with molecular, electrophysiological, and morphological features that clarify hybrid MSN identities. Comparative cis-regulatory analysis reveals conserved sequence grammars that encode cell identity and inform viral targeting strategies, providing a foundational resource for BG evolution, function, and disease.