The molecular pathways regulating lymphoid priming, fate, and development of multipotent bone marrow (BM) stem/ progenitor cells that continuously replace thymic progenitors remain largely unknown. Herein, we show that fms-like tyrosine kinase 3 (Flt3) figand (FI)-deficient mice have distinct reductions in the earliest thymic progenitors in fetal, postnatal, and adult thymus. A critical role of FL in thymopoiesis was particularly evident in the absence of interleukin-7 receptor alpha (IL-7R alpha) signaling. FI-/-II-7r(-/-) mice have extensive reductions in fetal and postnatal thymic progenitors that result in a loss of active thymopoiesis in adult mice, demonstrating an indispensable role of FL in IL-7R alpha independent fetal and adult T lymphopoiesis. Moreover, we establish a unique and critical role of FL, distinct from that of IL-7R alpha, in regulation of the earliest lineage-negative (Lin(-)) Lin(-)SCA1(+)KIT(+) (LSK) FLT3(hi) lymphoid primed multipotent progenitors in BM, demonstrating a key role of FLT3 signaling in regulating the very earliest stages of lymphoid progenitors.