Exercise has been shown to positively augment adult hippocampal neurogenesis; however, the cellular and molecular pathways mediating this effect remain largely unknown. Previous studies have suggested that microglia may have the ability to differentially instruct neurogenesis in the adult brain. Here, we used transgenic Csf1r-GFP mice to investigate whether hippocampal microglia directly influence the activation of neural precursor cells. Our results revealed that an exercise-induced increase in neural precursor cell activity was mediated via endogenous microglia and abolished when these cells were selectively removed from hippocampal cultures. Conversely, microglia from the hippocampi of animals that had exercised were able to activate latent neural precursor cells when added to neurosphere preparations from sedentary mice. We also investigated the role of CX 3 CL1, a chemokine that is known to provide a more neuroprotective microglial phenotype. Intraparenchymal infusion of a blockingantibodyagainsttheCX 3 CL1receptor,CX 3 CR1,butnotcontrolIgG,dramaticallyreducedtheneurosphereformationfrequencyinmice thathadexercised.WhileanincreaseinsolubleCX 3 CL1wasobservedfollowingrunning,reducedlevelsofthischemokinewerefoundintheaged brain.LowerlevelsofCX 3 CL1withadvancingagecorrelatedwiththenaturaldeclineinneuralprecursorcellactivity,astatethatcouldbepartially alleviated through removal of microglia. These findings provide the first direct evidence that endogenous microglia can exert a dual and opposing influence on neural precursor cell activity within the hippocampus, and that signaling through the CX 3 CL1-CX 3 CR1 axis critically contributes toward this process.