Memory formation depends on changes in gene expression, which are often resulting from epigenetic modifications. The Drosophila mushroom body (MB) is an ideal model to study this question thanks to its well-characterized role in learning and memory, and the wide array of genetic tools available to target specific neuron types. The MB is divided into the gamma, alpha’/beta’, and alpha/beta lobes, with roles in memory acquisition, reinforcement, and retrieval, respectively. We wondered whether the different functions of these lobes are accompanied by significant changes at the chromatin level. To address this, we took advantage of Chromatin Targeted DamID and used a representative set of chromatin-binding proteins to group chromatin into distinct states, to which we have added Tip60, a histone acetyltransferase implicated in Alzheimer’s disease. We targeted this profiling approach to the whole MB or different lobes with specific Janelia Farm Gal4 lines and compared them to a pan-neuronal line for reference. Binding of RNA polymerase II showed an enrichment of know MB genes in our MB samples, thus validating the specificity of our approach. Here, we show that the chromatin landscape of MB neurons differs from all other neurons within the brain, and also exhibits lobe to lobe remodelling. We further demonstrate that Tip60 is predominantly associated with the non-TrxG active/Yellow chromatin state, which mainly contains metabolic and housekeeping genes.