Seasonal variations in immune functions point toward the involvement of melatonin in its regulation. These chronobiotic effects are exerted by receptors present on the immunocompetent cells. The present study investigated daily/nycthemeral variation in expression of melatonin receptor subtypes MT1/MT2 in the lymphoid organs (spleen/thymus) of a tropical squirrel, Funambulus pennanti. The receptor expression was noted every 4 h interval over 24 h under natural light-dark cycle, during two seasons and was correlated with peripheral level of melatonin. The MT1/MT2 receptor expression displayed higher levels at the time of dusk (light-dark transition; 1800 hours), while plasma melatonin was still low compared to the preceding time point. The receptors were downregulated during the nighttime with a minimum expression at 0200 hours. Thymus, during the long day length, showed a tissue-specific pattern of receptor expression with a minimum expression at 0600 hours. Results suggest that photoperiod by modulation of melatonin level inversely regulates the receptor expression. The observations imply that there exists a temporal window of sensitivity in the target organs to the melatonin signal that is regulated by modulation of melatonin receptor expression which might be involved in mediating the photoperiodic effects of melatonin in the control of seasonal immune physiology.