Basophils and mast cells have long been known to play critical roles in allergic disease and host defense against parasitic infections. Recent recognition of these effector cells in immune regulations, host defense against bacteria and virus, and autoimmune diseases entices increased interest in studying these cells. However, origin and molecular regulation of basophil and mast cell differentiation remain incompletely understood. In this review, we focus on recent advances of the understanding the origin and molecular regulation of mouse basophil and mast cell development. We also summarize progress in the understanding of the origin and molecular regulation of human basophil and mast cell development. A more complete understanding of molecular regulation of basophils and mast cells will lead to the development of interventions that are more effective in achieving long-term success.