Vascular system pathology is a precipitating factor in numerous diseases lacking effective treatment. Advancing our understanding of the cell types that comprise the vascular system opens new therapeutic avenues for these diseases. Two key vascular cell types are endothelial cells (ECs) and pericytes. ECs form a monolayer lining the lumen of all vessels and are essential to vascular function. Pericytes lie atop the EC monolayer, sharing a basement membrane. Together, ECs and pericytes preserve vascular integrity, regulate blood flow, mediate immune cell trafficking, and control the exchange of molecules between the bloodstream and surrounding tissues. Recent advances in integrative single-cell transcriptomics and epigenomic profiling have facilitated tackling critical questions about ECs and pericytes. In this work, we examined EC transcriptional heterogeneity and interrogated the transcriptional and regulatory mechanism that control pericyte identity. Utilizing zebrafish (Danio rerio) as the model animal, single-cell RNA sequencing (scRNA-seq) of ECs followed by transgenic-reporter validation, revealed anatomical and function specific transcriptional signatures of ECs across the vascular tree. Parallel scRNA seq and single nucleus ATAC seq of pericytes identified notch3 as the central transcriptional hub in pericytes. Enhancers containing RBPJ DNA-binding motifs were sufficient to drive reporter expression in pericytes, while CRISPR-mediated disruption of these motifs abolished activity, demonstrating their necessity in vivo. Genetic analyses confirmed notch3’s essential role in pericyte development and uncovered an additional, non-redundant role for jag2b. These findings expand the molecular atlas of vascular cell types and uncover mechanisms by which notch3 maintains pericyte identity, offering new entry points for therapeutic modulation of vascular disease.