Significance People with multiple sclerosis have a microbiota distinct from healthy controls, and there is growing interest in how these differences might contribute to the onset and progression of CNS autoimmunity. However, the impact that the microbiota may also have on the endogenous regeneration of myelin—remyelination—has not yet been explored. Here we show that inflammatory responses during remyelination depend upon the microbiota, being modulated by antibiotics or probiotics or in germ-free mice. In contrast, these interventions had minimal impact on the activity of oligodendrocyte progenitor cells, with only supratherapeutic doses of antibiotics having an inhibitory effect. Our results suggest that endogenous CNS remyelination is largely resilient to interventions that modify the microbiota.