Abstract: To investigate the relationship of genes expression between brain tissue and ovary development, and explore more functional genes of Platichthys stellatus, total RNA from the mixed sample of pituitary gland and hypothalamus at the ovary maturation and degradation stages were isolated and sequenced by HiSeq 2000 high throughput sequencing technology. After assembly and splicing, 24128 unigenes from a total of 30640 unigenes were annotated based on the blast homology alignment. All 29137 unigenes with eggNog annotations were divided into 26 categories that were involved in physiological processes, such as signaling transduction, translation mechanism, etc. The results from KEGG pathway analysis showed that all unigenes at the ovary maturation stage were involved in metabolic pathways with 135 up-regulated sequences, while the unigenes at the ovary degradation stage were associated with 192 metabolic pathways with 648 up-regulated sequences. Moreover, 334 differentially expressed genes (DEGs) were up-regulated at the ovary maturation stage, while 987 up-regulated DEGs were observed at the ovary degradation stage. Total 408 unigenes were involved in reproductive and endocrine regulation, and 1508 unigenes were involved in signaling molecules. The expression of some reproduction-associated DEGs including growth hormone releasing hormone (GnRH), neurokinin B (NKB), gonadotropin (GtH), follicle stimulating hormone (FSH), kisspeptin (Kiss), and prolactin-relea-sing peptide receptor (PrRPR) were verified by qRT-PCR. All genes except FSH were consistent with the results of the transcriptome sequencing.