Abstract: Sturgeon, one of the oldest chondrostei in the world, has no sexual dimorphic appearance. To understand the molecular characteristics of the gonad development of sturgeon under artificial culture, characteristics of mRNA levels between the testis and ovary of two-year-old Amur sturgeon (Acipenser schrenckii Brandt) were analyzed using transcriptome sequencing. A total of 19690 differentially expressed gene transcripts were found between the gonads, in which the sex-related genes mainly included three transcription factors (Dmrt1, Sox9 and Foxl2) and three transforming growth factors (Amh, Bmp15 and Gdf9). We found four significant enrichment KEGG pathways involved in the process of ovarian development: progesterone-mediated oocyte maturation, oocyte meiosis, ovarian steroidogenesis and the GnRH signaling pathway. The expression patterns of 18 differentially expressed genes in the ovarian steroidogenesis pathway were analyzed. The results suggest that estrogen biosynthesis is inhibited in the ovaries of two-year-old Amur sturgeon. However, androgen biosynthesis is not affected in the testis. This study provides a foundation for studies on gonadal differentiation, the development of sturgeon, and sex identification at the level of mRNA expression.