The muskrat (Ondatra zibethicus L.) is a seasonal breeding animal. Adult male muskrat has a pair of scent glands between the muscle and skin above the urogenital tract, which secrete muskrat musk during the breeding stage. Compared with other rodents, the muskrat prostates and seminal vesicles are very well developed throughout the breeding stage. Studies have shown that intraperitoneal injection of muskrat musk can readily promote the development of the prostates and seminal vesicles in the male mice, suggesting a tight correlation between musk secretion and the development of the prostates and seminal vesicles in the muskrat. In this study, RNA-seq technology was used to analyze the gene expression patterns were further investigated by gene ontology (GO) analysis and KEGG pathway analysis. The results showed that 1629 genes were significantly and differentially expressed and were involved in a variety of signal transductions and energy metabolism pathways. The differential expression patterns of the OBP2 gene, and members of the Bcl-2 family and tumor necrosis factor receptor superfamily suggest that the prostate development in muskrat is controlled by a variety of molecular mechanisms; and the musk secreted by the muskrat scent glands might participate in the regulation of such developmental processes.