Reproductive organs are among the most variable and rapidly evolving structures in the animal kingdom, probably due to sexual selection. In insects, the diverse morphology of male genitalia is often one of the few visible characteristics that can reliably distinguish closely related species, making it crucial for taxonomic classification. Consistent with this, males of the model organism Drosophila melanogaster and its closely related species display remarkable variations in genital morphology. This variation has made the male genitalia of Drosophilids an invaluable system for dissecting the genetic and developmental pathways responsible for morphological evolution, providing insights into how new structures emerge and how gene regulatory networks are co-opted during this process. In this review, we highlight recent studies that have uncovered developmental processes, novel genes, and regulatory networks that contribute to the morphogenesis and evolution of these extraordinary structures. These studies mark a significant advancement in our understanding of the mechanisms driving the evolution of complex organs.