In order to identify candidate genes involved in ovary development, Illumina Hiseq technology was used to define the transcriptome of spotted steed brain, ovary and liver. A total of 49 484 132, 47 540 538 and 50 622 304 clean reads were generated from brain, ovary and liver, and then assembled into 99 878 Unigenes with an average length of 1 430 bp. DEseq analysis revealed that 2 305 were found only in the expression of brain vs. ovary group, 839 were found only in the expression of brain vs. liver group, 1 474 were found only in the expression of ovary vs. liver group, and 860 genes were found to be co-expressed in the three comparison groups. Gene ontology analysis indicated that many of these genes encoded proteins involved in primary metabolic process, single-organism process, organic substance metabolic process. Based on KEGG pathway analysis, putative genes are novel candidate regulators of oocyte development and meiosis, such as GnRH signaling pathway, Steroid hormone biosynthesis, TGF-beta signaling pathway and Oocyte meiosis. The spotted steed transcriptome data reported here will provide valuable new data to increase genomic resources of this species. The data will also provide a valuable basis for further reproductive molecular biology studies of this commercial species.