Prostaglandins (PGs) serve as signaling molecules that regulate various physiological processes, including inflammation, immune response, blood clotting and reproduction. The aim of this study was to investigate the immunolocalizations and expression patterns of prostaglandin-E2 (PGE2), cyclooxygenase (COX)-1 and COX-2, as well as its receptor subtypes 4 (EP4) in the scent glands of muskrats (Ondatra zibethicus) during the breeding and non-breeding periods. There were significant seasonal differences in the scent glandular mass, with higher values in the breeding season and relatively low in the non-breeding season. PGE2, EP4, COX-1 and COX-2 have been immunolocalized in the scent glandular and epithelial cells in both breeding and non-breeding seasons, whereas no immunostaining was observed in the interstitial cells. The protein and mRNA expression levels of EP4, COX-1 and COX-2 were higher in the scent glands of the breeding season than those of the non-breeding season. The mean mRNA levels of EP4, COX-1 and COX-2 were positively correlated with the scent glandular weights. The circulating follicle stimulating hormone (FSH), luteinizing hormone (LH), testosterone (T) and PGE2, as well as scent glandular PGE2 and dihydrotestosterone (DHT) concentrations were also significantly higher in the breeding season. Additionally, the transcriptomic study in the scent glands identified that differentially expressed genes might be related to fatty carboxylic monocarboxylic acid, steroidogenic-related pathway and prostanoid metabolic process. These findings suggested that prostaglandin-E2 might play an essential autocrine or paracrine role in regulating seasonal changes in the scent glandular functions of the muskrats.