Granulosa cells surround the oocyte within the ovarian follicle and play an essential role in creating conditions required for oocyte as well as follicular development. The current study was conducted to examine the gene expression profile of mouse ovaries during the primordial to primary follicle transition process. Total RNAs from mouse ovaries on day 5 and day 12 were synthesized cDNA using annealing control primers. The DEGs were cloned and their identities were analyzed by BLAST search. The Plekha5 and Anxa11 were highly expressed in primary follicle stage. By contrast, their expression was increased in granulosa cells at the primary follicle stage. We have successfully discovered a list of genes expressed in day 5 and day 12 ovaries and confirmed that some of them are differentially expressed in PMF and/or PRI. This is a spatial-temporal regulatory mechanism on the ovarian folliculogenesis through membrane fusion. The gene expression profile from the current study would provide insight for future study on the mechanism(s) involved in primordial-primary follicular transition. This will provide information for identification of the mechanism of ovarian dysfunction.