The cellular compartment of the adult rodent subependymal zone (SEZ)-neurogenic niche is the most active regenerative area of the brain and of great interest to the regenerative medicine field. It is complex and highly heterogeneous, including neural stem cells (NSCs) in different states of activation, rapid-amplifying progenitors, immature neuroblasts (NBs), mature neurons and other non-neurogenic populations. This chapter provides a step-by-step overview of a versatile flow cytometry-based protocol, which has been molecularly and functionally validated to classify and isolate the complete neurogenic lineage, including three NSC fractions (quiescent, primed, and activated), without the need for reporter mice. The panel is adaptable to diverse fluorescence needs and different cell targets, including niche differentiated cells such as endothelial cells, oligodendrocytes, or microglia, enabling the identification and isolation of the vast majority of cell types present in the SEZ. Additionally, it allows the study of cell cycling dynamics by means of 5-ethynyl-20-deoxyuridine (EdU) incorporation. The method enables the isolation of the different SEZ fractions and the functional assay of their cycling heterogeneity, including quiescence-activation transitions of NSC.