The Anatolian ground squirrel (Spermophilus xanthoprymnus) is a typical example of true mammalian hibernators. In order to adapt to extreme external and internal environments during hibernation, they lower their body temperatures, heart rates and oxygen consumption; however, pathological events such as ischemia and ventricular fibrillation do not occur in their cardiovascular systems. During the hibernation, maintenance of cardiac function is very important for survival of ground squirrels. Natriuretic peptides (NPs) are key factors in the regulation of cardiovascular hemostasis. Since NPs’ role on the protection of heart during hibernation are less clear, the aim of this study was to investigate dynamic changes in NPs content in the cardiac chambers and to reveal the possible role of NPs on establishing cardiac function in ground squirrel during hibernation using immunohistochemistry. The immunohistochemical results indicate that cardiac NP expressions in atrial and ventricular cardiomyocytes were different from each other and were sex-independent. ANP and BNP were expressed in a chamber-dependent manner in female and male squirrel hearts. Furthermore, cardiac NPs expression levels in hibernation period were lower than those at the pre-hibernation period. During prehibernation period, ANP, BNP and CNP were expressed in the white and beige adipocytes of epicardial adipose tissue (EAT); while during hibernation period, the brown adipocytes of EAT were positive for BNP and CNP. These data suggest that the hibernation-dependent reduction in levels of NPs, particularly ANP, in cardiac chambers and EAT may be associated with low heart rate and oxygen consumption during hibernation. However, further studies are needed to better delineate the roles of NPs during the hibernation.