Stem cells have the ability to switch between proliferative (self-renewal) and differentiation modes. The Drosophila germarium is a well-established in vivo model for the study of communication between stem cells and their niche. One commonly used technique for such study is immunostaining that allows examination of protein localization at a fixed time point. This chapter provides a detailed protocol for immunofluorescence staining of Drosophila ovaries. This protocol has been optimized to enable explicit visualization of the niche structure, as well as to maximize the degree of multiplexing for protein labeling and detection.