Microglia are the prototypical innate immune cells of the central nervous system. They constitute a unique type of tissue-resident mononuclear phagocytes which act as glial cells. Elegant experiments in the last few years have revealed the origin, extraordinary molecular diversity, and phenotypic plasticity of these cells and how their potential relates to both immune and non-immune actions in the normal and diseased brain. Microglial cells originate in the yolk sac and colonize the brain during embryogenesis, playing a role in neural development and later in adult brain function. Neurogenesis continues after birth in discrete areas of the mammalian brain sustained by the postnatal persistence of neural stem cells in specific neurogenic niches. Recent data indicate that microglial cells are distinct cellular elements of these neurogenic niches where they regulate different aspects of stem cell biology. Interestingly, microglial and neural stem cells are specified very early in fetal development and persist as self-renewing populations throughout life, suggesting potential life-long interactions between them. We aim at reviewing these interactions in one neurogenic niche, the subependymal zone.