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The ovaries, the main female reproductive organs, directly mediate ovulation and reproductive hormone secretion. These complex physiological processes are regulated by multiple genes and pathways. However, there is a lack of research on goat ovaries, and the molecular mechanisms underlying the signaling pathways remain unclear. In this study, Illumina HiSeq 4000 sequencing was used to sequence the transcriptomes of goat ovaries. The expression patterns of differentially expressed mRNAs in goat ovaries at both the follicular and luteal phases were determined by bioinformatics analysis. A total of 1,122, 014, 112 clean reads were obtained, and 3770 differentially expressed mRNAs were identified for further analysis. There were 1727 and 2043 upregulated mRNAs in the luteal phase and follicular phase, respectively. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, some mRNAs that were highly expressed in ovaries during the luteal phase, such as HSD17B7, 3BHSD, and SRD5A2, may be related to the synthesis of progesterone. In addition, some mRNAs that were highly expressed in ovaries during the follicular phase, such as RPL12, RPS13 and RPL10, are related to the growth and maturation of oocytes. Taken together, the findings of this study provide genome-wide mRNA expression profiles for goat ovaries at the follicular and luteal phases and identify mRNAs associated with goat hormone secretion and follicular development. In addition, this study provides a theoretical basis for further investigation of goat reproductive regulation., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2020. Published by Elsevier Inc.)