The advancement ofDrosophilagermline stem cell research accompanies the development of powerful new tools for genetic analysis. These include the techniques of stem cell labeling, cell lineage tracing, mosaic mutant analysis, and gene manipulation in targeted cell populations, which together constitute the critical methodologies in stem cell research. We discuss four such techniques: thetubulin-lacZpositive-labeling system; the positively marked mosaic lineage (PMML) method; the flipase/flipase recombination target (FLP/FRT)-based mosaic mutant analysis; and theGAL80-based mosaic analysis with a repressible cell marker (MARCM) system.