Chronic stress disrupts reproductive efficiency. Yet, the manner in which stress disturbs reproduction in goats is currently unknown. The Oaxacan Mixteca region is one of Mexico's poorest, with high levels of deforestation, high ambient temperatures, and lack of water. Native goats of the Oaxacan Mixteca Region live in these stressful conditions, as well as in overcrowded and water restricted conditions. Therefore, the aim of this study was to evaluate the effects of these very stressful conditions on the reproduction of male and female goats. Control group was uncrowded, with daily water supply; stress group was overcrowded, with water restriction. The study was conducted from September 2015 to February 2016; the expression of reproductive behaviour and variations of cortisol levels were assessed. In females, oestradiol and progesterone were evaluated during the oestrous cycle. In males, testosterone levels were evaluated before and during reproductive activity. Sexual behaviour decreased in stressed goats: approaching, tail swishing, urination, vaginal discharge and flank contraction decreased in stressed females. Anogenital sniffing, licking, Flehmen reflex, bleating, mount attempts and mounts decreased in male goats. Cortisol levels in stressed animals were higher compared with control animals. Oestradiol and Progesterone levels in stressed females were significantly lower during the follicular and luteal phase, respectively, compared with control females. Testosterone levels in stressed males were lower than in control males, both before and during reproduction. These results indicate that even though goats from the Oaxacan Mixteca Region are habituated to their environmental conditions, they are still stressed by them, as shown by a higher activation of the adrenal axis in stressed goats than in control goats. High cortisol levels may induce low oestradiol levels in females and low testosterone levels in males, as well as a disruption in the expression of their reproductive behaviour.