Cell types are fundamental units of metazoans, however, their definition remains a long-standing challenge. We here use high-throughput assays allowing for unprecedented resolution to analyze and compare the transcriptional landscapes of related and unrelated Drosophila cell types at larval and embryonic stages. Unexpectedly, all cell types share a stage-specific signature that is even stronger than the cell-specific one. Despite having distinct developmental origins and functions, neurons, glia, and hemocytes are more transcriptionally similar to one another within the same developmental stage than they are to the same cell type at different stages. This stage-specific signature is enriched for DNA repair genes at larval stage, particularly the MRN complex (Mre11-Rad50-Nbs). Loss of Rad50 disrupts histone modification patterns and causes inappropriate reactivation of embryonic gene expression programs in larval central nervous system (CNS), as revealed by transcriptomic and chromatin accessibility analyses. The identification of cell-specific and stage-specific signatures highlights a new dimension in the definition of cell identity and suggests a role for Rad50 in maintaining developmentally appropriate chromatin states.