Circadian rhythm is a biological rhythm that is related closely to the rhythmic expression of a series of clock genes. A number of studies have revealed the role of circadian rhythms in the estrous mode of mammals. In the present study, the expression patterns of six canonical clock genes (Clock, BMAL1, Cry1, Cry2, Per1 and Per2) were analyzed in year-round estrous rams (Small Tail Han sheep, STH) and seasonal estrous rams (Sunite sheep, SNT). The result showed that all six genes were expressed in brain, cerebellum, hypothalamus, pituitary, testis, epididymis, vas deferens and adrenal gland tissues in both breeds. The expression level of Clock and BMAL1 showed similar trends in the brain, cerebellum, hypothalamus, pituitary, testis and epididymis in both breeds. The expression levels of Clock, BMAL1, and Cry1 were significantly higher in the pituitary tissue of STH rams than in that of SNT rams, whereas the expression level of Cry2 showed the opposite pattern. We speculate that Cry1 and Cry2 may have opposite roles in the circadian rhythm of rams. Moreover, the expression patterns of Cry1/2 and Per1/2 in the pituitary suggested that the CRY and PER proteins may function in the circadian rhythm either as a complex or as individual, Therefore, we concluded that circadian rhythmicity may regulate the estrous mode of rams via clock genes within transcription/translation feedback/feedforward loops. This is the first study to systematically analyze the expression patterns of clock genes in rams.