Seasonal cycles in breeding, often orchestrated by annual changes in photoperiod, are common in nature. Here, we studied how change in photoperiod affects DNA methylation in the testes of a highly seasonal breeder: the Siberian hamster (Phodopus sungorus). We hypothesized that DNA methylation in promoter regions associated with key reproductive genes such as follicle-stimulating hormone receptor in the testes is linked to breeding and non-breeding states. Using Oxford Nanopore sequencing, we identified more than 10 million (10,151,742) differentially methylated cytosine-guanine (CpG) sites in the genome between breeding long photoperiod and non-breeding short photoperiod conditions. ShinyGo enrichment analyses identified biological pathways consisting of reproductive system, hormone-mediated signalling and gonad development. We found that short photoperiod induced DNA methylation in the promoter regions for androgen receptor (Ar), estrogen receptors (Esr1, Esr2), kisspeptin1 receptor (kiss1r) and follicle-stimulating hormone receptor (Fshr). Long photoperiods were observed to have higher DNA methylation in promoters for basic helix-loop-helix ARNT-like 1 (Bmal1), progesterone receptor (Pgr) and thyroid-stimulating hormone receptor (Tshr). Our findings provide insights into the epigenetic mechanisms underlying seasonal adaptations in timing reproduction in Siberian hamsters and could be informative for understanding male fertility and reproductive disorders in mammals.