Quarantines prevent infectious disease spread during primate transport, fostering acclimatisation. Environmental stress can lead to altered physiology, health risks, and epigenetic changes in other primates. We analysed PeruvianSaguinus fuscicollisandSaimiri macrodon, immobilised for 10 months in quarantine during the COVID-19 crisis, and compared them to wild counterparts to determine effects of quarantine as a stressor in New World monkeys.MethodsBoth quarantine and wild samples were collected from two riverine islands near the city of Iquitos, situated in the Peruvian Amazon (Island Muyuy and Padre Island). Cortisol levels in hair were quantified using ELISA (n=37; quarantine n=16; wild=21), and global DNA methylation levels were assessed for epigenetic comparison in dried blood spots (n=45; Quarantine: n=23; Wild: n=22), also utilising ELISA. Two-way ANOVA was employed to explore the effect of quarantine on cortisol and DNA methylation, considering the effect of species, and sex differences on these measurements.ResultsCortisol analysis revealed a significant association between quarantine and elevated cortisol secretion when testing both species together and independently, with a greater difference between quarantine and wild forSaguinus fuscicollis. Quarantine was associated with global DNA hypomethylation when testing both species together, however, independent ANOVAs show there was no effect of quarantine onSaguinus fuscicollis, and a marginal significant effect of quarantine onSaimiri macrodon.DiscussionNew World monkey species displayed hormonal and epigenetic dysregulation 10-months after starting quarantine period, suggesting long-term physiological and genomic stress as a response to captivity. Species specific differences in stress adaptability might mediate observed effects.