Present in all organs, mononuclear phagocytes consist of a heterogeneous population of hematopoietic cells whose main role is to ensure tissue homeostasis through their ability to scavenge cell debris, promote tissue repair and maintain tolerance to self-antigens while simultaneously inducing innate and adaptive immune responses against foreign antigens that breach the tissue. The intestinal mucosa is particularly exposed to foreign antigen, through constant exposure to high loads of commensal bacteria and dietary antigens as well as providing a site of entry for viral and bacterial pathogens. The molecular mechanisms that control the intestinal ability to distinguish between "innocuous" and "dangerous" antigens remains poorly understood although it is clear that mononuclear phagocytes play a key role in this process. This review highlights recent advances in our understanding of heterogeneous origin of the mononuclear phagocytes that inhabit the intestinal mucosa and discusses how developmental diversity allows for functional diversity to ensure intestinal integrity.