Inhibitory photoperiod differentially effects reproduction in deer mice (Peromyscus maniculatus nebrascensis). Pituitary-testicular function is arrested in about one-third of short-day exposed males (reproductively responsive mice), while an equal number remain fertile (reproductively nonresponsive mice). Both phenotypes are found in natural populations and their disparate reproductive responses have a genetic basis. To assess whether this difference is attributable to a prepineal/pineal or post-pineal mechanism, we compared spermatogenic responses of known and unknown phenotype to exogenous melatonin. Melatonin significantly reduced mean sperm number in long-day housed mice of unknown phenotype. But, individual responses ranged from azoospermia to normal spermatogenesis, and this range was not significantly different from that previously recorded for short-day exposed mice. Reproductively nonresponsive males were unaffected by melatonin administration when housed under long or short daylength. In contrast, melatonin significantly suppressed sperm production in reproductively responsive males housed under long photoperiod, but had no additional suppressive effect in short-day housed mice with regressed testes. These data demonstrate that melatonin is only effective in eliciting testicular regression in reproductively responsive males. Taken together, these results suggest that differential testicular response to photoperiod are caused by a post-pineal mechanism.