Hypothalamus are the important endocrine organs, which play key roles in regulating body growth, reproduction and hormone activity in other endocrine glands and organs. Estrogen, an important sex steroid hormone, is mainly synthesized and secreted in the gonads. It could regulate the reproduction and growth related genes expression in hypothalamus through feedback, and then participate in the regulation of corresponding physiological activities. Spotted scat (Scatophagus argus) is a good model to investigate the sexual growth dimorphism with a faster growth in females than males. The effect of 17β-estradiol (E2) injection in vivo on genes expression in hypothalamus of XY male spotted scat and the differences in genes expression between XY males and XX females remain unclear. In order to explore gene expression difference between XY male and XX female spotted scat hypothalamus and effect of in vivo injection in XY males, transcriptome analysis of hypothalamus were carried out, including sequencing data quality control, gene function annotation, differentially expressed gene (DEGs) screening and identification and pathway enrichment analysis, then real-time quantitative PCR (qPCR) was performed to detect genes expression. A total of 275833710 Clean reads were sequenced in this study, and the Q30 and GC value were more than 95% and 48%, respectively. In Ctrl-XX-H vs. Ctrl-XY-H group, 91 DEGs were screened and identified successfully, including 36 up-regulated and 55 down-regulated genes. In Ctrl-XX-H vs. E2-XY-H group, 28 DEGs were screened and identified, including 11 up-regulated and 17 down-regulated genes. GO and KEGG pathway analysis showed that DEGs was significantly enriched in biological processes such as cells, single cell, membrane, membrane components, and signal pathways such as ubiquinone and other terpene quinone biosynthesis, steroid hormone biosynthesis. By transcriptome and qPCR analyses, the expression of nrip1b, prl, hspa8b, snx21, cep63, ccna1, hsp90aa1.1, slc1a5, zar1, slc25a1b and loc124068175, were significantly different between XX and XY spotted scat, while the reproductive axis genes (sbGnRH, sGnRH and cGnRH) and growth axis genes (ghrh, sst1, sst3, sst5 and sst6) expression showed no significant differences. In XY male fish, six hours after E2 injection, the expression of cdc42ep1a, cyp19a1b, greb1, kank1a, snx21, and tmem30c in hypothalamus were significantly up-regulated, while prl expression was significantly down-regulated. Above results suggest that E2 might regulate some reproduction related genes expression in hypothalamus through feedback effects, which plays the critical roles in gametogenesis and reproduction regulation. [ABSTRACT FROM AUTHOR]