Abstract: 【Objective】The candidate genes and pathways related to the ovarian development of Trachinotus ovatus were identified,so as to lay the foundation of revealing the molecular mechanism on ovarian sexual maturation.【Method】 The stage І and stage Ш ovarian tissue of T. ovatus were selected to construct the cDNA library for stage І and stage Ш,respectively. Transcriptome sequencing was performed by Illumina HiSeq^TM2005. After filtering,quality control,and assembly,the unigenes obtained were mapped to the seven databases(Nr,Nt,Pfam,KOG/COG,Swiss-Prot,KEGG and GO). The differentially expressed genes(DEGs)were identified by FPKM and DEGseq. The GOseq and KOBAS were used for functional annotation and signal pathway enrichment analysis of DEGs,respectively. And the simple sequence repeat(SSR)identification and single nucleotide polymorphisms(SNP)analysis were performed by MISA and gatk3.【Result】The results showed that a total of 325156432 raw reads were generated from ovarian tissues. After filtering,317206752 clean reads were selected,and then were assembled into 59554 unigenes,69.65% of which were successfully annotated in Nr,Nt,Pfam,KOG/COG,Swiss-Prot,KEGG and GO databases. 24599 and 15997 unigenes were annotated to the GO database and KEGG database,respectively. The analysis showed that a total of 17737 DEGs were found in the ovaries of T. ovatus,among which 8169 DEGs were up-regulated at stage Ш ovary,and 9568 DEGs were down-regulated in stage Ш ovary. The GO functional annotation analysis demonstrated that,cellular process,nitrogen compound metabolic process,primary metabolic process,nucleus,nuclear part,ion binding and hydrolase activity. The results of KEGG signaling pathway enrichment analysis showed that 17737 DEGs were significantly enriched on 318 metabolic pathways. The top 20 KEGG signaling pathway including 2-Oxocarboxylic acid metabolism,PI3K-Akt signaling pathway,thyroid hormone signaling pathway,phospholipase D signaling pathway,Fc epsilon RI signaling pathway and cell cycle. Finally,a total of 30133 SSRs and 82490 SNPs were obtained from the 59554 unigenes of ovarian transcriptome of T. ovatus.【Conclusion】Six DEGs,including GnRHR,FSHR,FSHβ,CYP11A,SIRT3 and PEG3,as well as two KEGG pathways such as PI3K-Akt signaling pathway and VEGF signaling pathway are closely involved in the ovarian development of T. ovatus,which co-regulates ovarian development and maturation.