A new single-cell reference atlas for the starlet sea anemone Nematostella vectensis has been developed, providing a comprehensive transcriptomic inventory of 127 distinct cell states, including 47 neuroglandular subtypes. The study re-mapped previously published single-cell transcriptomic data to a new chromosome-level genome assembly and gene models, improving gene annotations and enabling more accurate identification of cell states. The atlas includes data from four additional samples, expanding the dataset and revealing detailed transcriptomic profiles of various cell types, including epithelial, gastrodermal, and retractor muscle cells. The analysis highlights the maturation of cell states across developmental stages and identifies two distinct immune-related transcriptomic profiles. The study also identifies key cell types, such as the apical organ cells, and provides insights into the development of the nervous system and immune responses. The new gene annotation, Nv2, significantly improves the mapping of single-cell transcriptomic data and is available for public use. The atlas is accessible via the UCSC single-cell web browser and includes detailed gene expression data, marker genes, and regulatory profiles. The study underscores the importance of high-quality genome and gene annotations in single-cell transcriptomic analyses and provides a valuable resource for understanding cnidarian development and evolution.A new single-cell reference atlas for the starlet sea anemone Nematostella vectensis has been developed, providing a comprehensive transcriptomic inventory of 127 distinct cell states, including 47 neuroglandular subtypes. The study re-mapped previously published single-cell transcriptomic data to a new chromosome-level genome assembly and gene models, improving gene annotations and enabling more accurate identification of cell states. The atlas includes data from four additional samples, expanding the dataset and revealing detailed transcriptomic profiles of various cell types, including epithelial, gastrodermal, and retractor muscle cells. The analysis highlights the maturation of cell states across developmental stages and identifies two distinct immune-related transcriptomic profiles. The study also identifies key cell types, such as the apical organ cells, and provides insights into the development of the nervous system and immune responses. The new gene annotation, Nv2, significantly improves the mapping of single-cell transcriptomic data and is available for public use. The atlas is accessible via the UCSC single-cell web browser and includes detailed gene expression data, marker genes, and regulatory profiles. The study underscores the importance of high-quality genome and gene annotations in single-cell transcriptomic analyses and provides a valuable resource for understanding cnidarian development and evolution.