Evolutionary adaptations of brain structure and function are essential for animal survival and emerge during development. However, the cellular and genetic mechanisms controlling diversification remain enigmatic. In holometabolous insects, larvae differ from the adult in both behavior and brain morphology due to the divergent needs of larval and adult life. To study brain diversification, we used homology-directed genome editing to establish transgenic lines that visualize homologous cell groups throughout development with high precision in the fly Drosophila melanogaster and the beetle Tribolium castaneum. These genetic neural lineages have allowed us comparing the development of homologous neural cells from the embryo to the adult. Besides overall conservation, we detected conspicuous differences. Specifically, a part of the brain (the central complex) develops already in beetle embryos but only in pupae in flies. In the adult brain, we found cell clusters that diverge between those species. Finally, a clear change of retinal homeobox expression in the mushroom bodies might be linked to differences in adult neurogenesis between fly and beetle. We follow up these hypotheses by characterizing subpopulations of the genetic neural lineage by single cell sequencing and we are testing candidate regulator genes for their role in shifting developmental timing.