Objective Rhesus macaques have been widely used in studies on pathology, drugs and vaccines of human diseases,. To elucidate the biological characteristics of the type Ⅲ interferon system of these monkeys, the expression of IFNLs and IFNLR1 in the genital tract of rhesus macaques was examined. Methods Gene specific RT-PCR methods were established to observe the expression levels of IFNL1, IFNL3, and IFNLR1 mRNA in normal and immunodeficiency virus infected genital tract tissues of rhesus macaques, the distribution of IFNLR1 immunoreactivity in these tissues was examined by confocal microscopy. Results It was found that the levels of IFNL1 and IFNL3 mRNA in the uterus and vagina of normal rhesus macaques are under the threshold of the methods, while the mRNA of IFNLR1 and its variant that lacking exon 6 could be readily detected. The immunoreactivity to IFNLR1 could be detected primarily in the covering or glandular epithelia of the uterus and vagina. Among the SHIV/SIV infected rhesus macaques, mRNA levels of IFNL1 and IFNL3 were increased in some individuals, mRNA levels of IFNLR1 were not changed, and mRNA levels of ISGs (Mx1, Mx2 and OAS) were increased significantly. Conclusions These data indicated that the type Ⅲ interferon system is expressed in the reproductive tract of rhesus macaques as in humans, which provided a scientific basis for using rhesus macaques in studies of human infectious diseases like AIDS.