Epigenetic modifications in reproductive tissues have predominantly focused on pathological conditions, such as ovarian and uterine cancers. The contribution of DNA methylation and histone acetylation to the timing and control of fertility is not well described. Siberian hamsters provide an important model to investigate the relatively short-term regulation of fertility (e.g. estrous) as well as long-term timing of breeding (e.g. seasonal). Recent work has shown that DNA methyltransferase 3a (dnmt3a) expression is associated with reproductive involution. Here, the objectives were to identify the impact of photoperiod on hdac1–3 expression in hamster testicular, ovarian and uterine tissue. Then, we assessed the effect of E2P4 and estrous cycling on hdac1–3 expression in uterine tissue. Testicular expression of hdac1 was significantly reduced, whereas hdac3 increased in reproductively photoregressed male hamsters; hdac2 expression did not significantly change across photoperiod conditions. There was no significant photoperiodic effect on ovarian expression of hdac1–3. Uterine expression of hdac3 expression was greater in long day hamsters; exposure to short days significantly reduced uterine hdac2 expression. Ovariectomized hamsters administered a single bolus injection of oil were found to have elevated uterine hdac2 compared to E2P4 treated females 12 h and 24 h post injection. Uterine hdac1–3 expression was relatively constant across the estrous cycle. Altogether these data indicate tissue-dependent photoperiodic regulation of hdac1–3 expression and that E2P4 may inhibit uterine hdac2 over long-term breeding cycles.