In female sheep fetuses, two of the most crucial stages of ovarian development are prophase of meiosis I and follicle formation. In the present study, sheep ovaries collected on Days 25, 38, 49, 56, 67, 75, 94, and 120 of gestation, at birth, and in adulthood were tested by reverse transcription-polymerase chain reaction (RT-PCR) for the expression of 14 genes known to be involved in the ovarian differentiation in diverse organisms. The aim of this study was to determine 1) the expression pattern of six genes involved in germ cell development or meiosis (DMC1, SPO11, MSH4, MSH5, DAZL, and Boule) and five ovary-derived factors (OVOL1, SIAH2, DIAPH2, FOXL2, and FGF9), 2) the onset of gene expression for several members of the bone morphogenetic protein (BMP) pathway involved in follicular development (GDF9, BMP15, BMPR-IB), and 3) the chromosomal localization of seven of these genes in the sheep genome. The RT-PCR analysis revealed that the two germline-specific genes, DAZL and Boule, were expressed between 49 and 94 days postcoitum (dpc) with a similar pattern to typical meiosis genes (DMC1, MSH4, and MSH5), suggesting their possible participation in prophase of meiosis I. GDF9 and OVOL1 gene transcription started at 56 dpc and extended until birth, while BMP15 presented a more restricted window of expression between 94 dpc and birth, corresponding to the formation of first growing follicles. The homologous ovine genes for SPO11, DMC1, MSH5, DAZL, FGF9, DIAPH2, and SIAH2 were located on OAR 13q21–22, 3q35, 20q22, 19q13, 10q15, Xq44, and 1q41–42, respectively. In sheep, quantitative trait loci affecting female reproductive capacities are currently being detected. The ontology and precise mapping of ovarian genes will be useful to identify potential candidate genes that might underlie these effects.