It is becoming clear that epigenetic modifications such as DNA methylation can be dynamic and in many cases, reversible. Here, we investigated the photoperiod and hormone regulation of DNA methylation in testes, ovaries and uterine tissue across multiple time scales. We hypothesized that DNA methyltransferase 3a (dnmt3a) is driven by photoperiodic treatment, exhibits natural variation across the female reproductive cycle and that melatonin increases whereas estrogen reduces DNA methylation. We used Siberian hamsters (Phodopus sungorus) due to their robust changes in reproductive physiology across seasonal and oestrus time scales. Our findings indicate that short day (SD) – winter like conditions significantly increased global DNA methylation and dnmt3a expression in the testes. Using immunohistochemistry, we confirm that increased dnmt3a expression was primarily localized to spermatogonium. Conversely, the ovaries did not exhibit variation in DNA methylation or dnmt3a/3b expression. However, exposure to SD significantly increased uterine dnmt3a expression. We then determined that dnmt3a was significantly decreased during the oestrus stage. Next, we ovariectomized females and subsequently identified that a single estrogen+progesterone injection was sufficient to rapidly inhibit dnmt3a and dnmt3b expression. Finally, we demonstrate that treatment of HEK293 cells with melatonin significantly increased both dnmt3a and dnmt3b expression suggesting that long-duration nocturnal signalling in SD may be involved in the regulation of DNA methylation in both sexes. Overall, our data indicate that dnmt3a shows marked photoperiod and oestrus plasticity that likely has broad downstream effects on the timing of the genomic control of reproductive function.