The reproduction of animals is a means to maintain their species. The golden hamsters are seasonal breeders, and their reproduction is regulated by the photoperiod. The shifts of the sexual functions imply the changes of the protein expression, and those are reflected by the proteome. Thus the present study was to examine via two dimensional polyacrylamide gel electrophoresis (2d PAGE), the physiological changes and the alterations of protein expressions in hypothalamus upon the reproductive situation related to the pineal gland. Among the pineal intact animals, the reproductive functions were sustained in animals housed in long photoperiod (LP) but regressed in animals housed in short photoperiod. And those pinealectomized animals showed high sexual activities regardless of photoperiod. Ultimately they were branched into dichotomy, sexually active and inactive animals. Apart from the changes of physiological parameters upon the reproductive conditions, there were obvious differences in proteins extracted from the hypothalamus. The hypothalamus of LP animals presented high levels of enzymes which are involved in the production of energy, glycolysis and Krebs cycle. The increased energy might be related to the GnRH synthesis in hypothalamus and indirectly to the constant cell divisions in spermatogenesis. Taken together, the impacts of the photoperiodic information controlling reproduction could be observed through 2d PAGE. Therefore, the present results suggest the potential of biomarkers collectively to diagnose the fertility and the infertility by way of proteomics in organs with regard to the reproductive system, further could be applied to diagnose various diseases.