Emerging and re-emerging infectious diseases pose a significant public health challenge, with severe economic, social, and health consequences. The frequency of epidemics caused by newly emerging and re-emerging pathogens and the likelihood of rapid global spread have increased dramatically in recent decades, with Southeast Asia considered a hot spot for future emergence events. Small mammals and bats play an important role in the maintenance and transmission of several zoonotic agents, such as filoviruses, coronaviruses, and henipaviruses. Cambodia is one of 35 global biodiversity hotspots that provides habitats for thousands of wildlife species, including over 70 species of bats. By proactively sampling animal populations in Cambodia to discern circulating parasitic genotypes and screening human sera for evidence of exposure, we aim to determine those parasites with human pathogenic potential. A standardised trapping regimen has been applied to allow us to understand ecological and environmental variables associated with host and parasite presence-absence, facilitating the creation of ecological niche maps and risk models to inform future surveillance efforts across Southeast Asia.