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Primordial germ cells (PGCs) development is a subtle and complex regulatory process. Fance is an important substrate molecule necessary for the activation of the Fanconi anemia (FA) pathway, and its homozygous mutant causes massive oocyte loss as early as embryonic day 13.5 (E13.5). Here, we present histological and RNA-seq analysis of Fance deficient PGCs to explore the possible mechanisms responsible for its progressive depletion of germ cells. In Fance^-/- embryos, the reduction of PGCs was already evident at E9.5 and the progressive loss of PGCs led to the PGCs being almost exhausted at E12.5. An increase of apoptotic cells was detected among Fance^-/- PGCs, which may intuitively explain their reduced number in embryos. Moreover, abnormal cell proliferation and accumulating DNA damage were detected in E12.5 Fance^-/- PGCs. We identified 3026 differentially expressed genes in E12.5 Fance^-/- PGCs compared to Fance^+/+ . KEGG pathway analysis revealed that the up-regulated genes were highly associated with ‘lysosome’, various metabolism pathways, whereas the down-regulated genes were mainly enriched in ‘cell cycle’, ‘oocyte meiosis’, ‘ribosome’, and various DNA repair pathways. In addition, multiple genes of various cell death pathways were found to be differentially expressed in E12.5 Fance^-/- PGCs, indicating that PGCs death in Fance^-/- embryos might diverge from canonical apoptosis. These findings indicate that Fance is essential for PGCs survival and the potential mechanisms involve cell cycle regulation, DNA damage repair, cell death prevention, and by regulating lysosome and ribosome function. Our results provide an important reference for further studies.