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Basophils and mast cells are major players in the progression of allergic disorders. Although both cell types originate from hematopoietic stem cells, their lineage commitment pathways and mechanisms have been unsolved issues in hematology. Recent advances in the multicolor FACS system enable the prospective isolation of progenitor populations whose readouts are restricted to basophil and/or mast cell lineages. These newly-isolated progenitor subsets are helpful to understand the developmental machinery of basophil and mast cell lineages, leading to the possible exploitation of a novel therapeutic strategy for allergic and autoimmune disorders. In this review, we summarize the recent progress in our understanding of the basophil/mast cell ontogeny on a cellular basis.