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In rodents, male-derived pheromones play fundamental roles in reproduction. The Hirosaki hairless rat (HHR) is a mutant strain derived from the Sprague–Dawley rat (SDR). While investigating the natural mating between single males and females, (SDR♂ x SDR♀) or (HHR♂ x HHR♀), the HHRs showed higher fecundity than the SDRs; the mean period between mating and delivery was shorter and every HHR pair gave birth, whereas approximately half of the SDR pairs gave birth in the 3 months of experimental testing. By changing partners between the HHRs and SDRs, (SDR♂ x HHR♀) or (HHR♂ x SDR♀), we attributed the fecundity difference to males. However, no significant difference was observed in the litter size, the concentration, morphology, or motility of sperm in the cauda epididymis, or the testosterone concentration in the serum between the SDR and HHR males. When an SDR and HHR male were simultaneously mated with a single female, the HHR males always succeeded in leaving progeny. Therefore, we assumed that the reason for the fecundity difference was the difference in copulation efficiency and focused on male-derived pheromones that may induce reproductive behaviors in females. Whereas Darcin (MUP20), one of the pheromones produced in the liver, did not appear to be involved, the extraorbital lacrimal gland (ELG) was heavier in the HHR males and showed larger amounts of pheromones, namely exocrine gland-secreting peptide 1 (ESP1) and cystatin-related protein 1 (CRP1). These results suggest that the fecundity difference is due to the difference in amounts of ELG-derived pheromones.