Organ systems in animals were shaped by adaptive processes on a macroevolutionary scale. Traditionally, macroevolution is in the scope of palaeontology, comparative morphology and evolutionary developmental biology (the so-called „evo-devo“ approach). Comparative genomics provides new levels of the analysis of macroevolutionary trends. Genomic phylostratigraphy is an innovative approach in this area of research, that could be used to trace important adaptive events in evolution. In the focus of this study is the phylostratigraphic analysis of organ systems in animals. For this purpose genomic and expression data from fruit fly (Drosophila melanogaster) was analyzed. Data suggest that some sort of central nervous system might be present in the eumetazoan ancestor. Also, support was found for the existence of a primitive form of heart in the bilaterian ancestor. Tracheal system analyses point to a possible common origin of tracheae and gills in the common ancestor of crustaceans and insects. Interestingly, a phylostratigraphic signal for the intestinal system is already present in the common ancestor of Metazoa. This work shows that phylostratigraphy could be effectively used in macroevolutionary analyses of complex phenotypes, such as organ systems. However, for a more complete understanding of their evolution, availability of a greater number of sequenced genomes, as well as more complete expression data, would be needed.