Environmental pollution is widespread and poses significant risks to both human populations and diverse animal species. As part of conservation initiatives, many endangered animals are housed in zoos and breeding centers close to human activities, potentially exposing them to health threats arising from environmental contamination, such as mercury (Hg). By analyzing non-invasive fecal samples from 13 Chinese zoos, we assessed total mercury (THg) and methylmercury (MeHg) exposure in two non-human primate species: the endangered species golden snub-nosed monkey (Rhinopithecus roxellana), and the most widely distributed rhesus macaque (Macaca mulatta). The concentration of THg in golden snub-nosed monkeys (mean ± s.d.: 76.7 ± 35.6 ng/g; median: 71.8 ng/g, range: 11.2–200.0 ng/g, n = 71) was significantly higher than that in rhesus macaques (mean ± s.d.: 32.3 ± 54.7 ng/g; median: 17.5 ng/g, range: 7.4–409.0 ng/g, n = 98). No significant differences were observed in both MeHg and MeHg % between these two species. Age and sex did not predict fecal Hg. Among adults, approximately 85 % of sampled individuals exhibited hazard quotient (HQ) values exceeding 1, indicating mercury poses a health risk to captive primate populations. The average HQ for golden snub-nosed monkeys was 2.98 ± 1.68 (range: 0.46–8.21, n = 43), while for rhesus macaques was 1.84 ± 1.64 (range: 0.61–12.49, n = 71). Our findings suggest that conservation efforts for captive primates may be compromised by Hg pollution, particularly in golden snub-nosed monkeys. Further investigation and ongoing biomonitoring from an ecotoxicological perspective, are crucial to ensuring the health of captive primate populations.