Gut microbiota is involved in the induction and functional maturation of various immune cells. However, there are only a few immune mechanisms that directly regulate gut bacteria. Immunoglobulin A (IgA) is a major immune mechanism which is important for the regulation of microbiota. It has been known for a long time that gut microbiota is critically involved in the induction of IgA. Recently, with the development of next-generation sequencing technologies, it has gradually been revealed that IgA also plays an important role in the regulation of the composition and function of gut bacteria. In this review, we introduce recent findings on the factors involved in the interaction between IgA and microbiota.