Drosophila melanogaster oogenesis is a versatile model system used to address many important questions of cell and developmental biology such as stem cell regulation, cell determination, cell polarization, cell-cell signaling, cell-cell adhesion, and cell-cycle regulation. The ovary is composed of germline and somatic cells of different origins and functions. Mosaic analysis using the powerful genetic tools available in Drosophila melanogaster allows deciphering the contribution of each cell type in the different processes leading to the formation of a mature egg. Germ cells and follicle cells are produced by actively dividing stem cells, which permit the use of recombinases, such as FLP, to generate genetic mosaics using mitotic recombination. This chapter summarizes the different methods used to create genetic mosaics in the germline and in somatic cells of adult ovaries. We briefly introduce the morphology and development of the adult female ovary. We then describe in practical terms how to generate mosaics with examples of cross schemes and recombining strains. We also explain how to identify the appropriate progeny and how to prepare clonal tissues for phenotypic analysis.