Southeast Asia (SE Asia) comprises 4% of the planet's land area but is home to approximately 25% of its terrestrial biodiversity. The region is one of the most geologically complex areas on Earth, creating many opportunities for population subdivision and, potentially, speciation. Unfortunately, research in SE Asia lags behind other tropical regions, and our understanding of the region has not improved despite lowering cost of molecular analyses. Research is critical to the understanding and conservation of species that are most threatened by human encroachment on natural habitats. This is doubly true for flying foxes, a genus of fruit-eating bats found only in the Old World, which are often hunted for sustenance in areas with low food security and mistakenly as crop pests. Flying foxes (Pteropus) serve many functions in the ecosystem, such as long-distance seed dispersal, but are also are natural hosts of animal-to-human diseases that we do not understand. If we are able to understand the natural history and migratory routes of flying foxes, we can use that knowledge to inform containment efforts in the event of a rare outbreak. Flying foxes are protected by the Convention for International Trade of Endangered Species (CITES) and their specimens cannot pass national borders without the proper permits. This has been one of the limits in conducting research on flying foxes. However, new methods can be developed with DNA extraction from fecal samples and abandoned food items, making it possible to conduct genetic analyses. These samples are not considered components of the bat and can be brought into the lab for further genetic testing. During my summer fellowship at the National University of Singapore in the lab of Prof. Meier, I was able to develop an efficient protocol using samples from the controlled environment of the Singapore Zoo. This method will be utile to all bat researchers who face logistic issues often in developing countries. I was also able to develop new genetic markers to add to the currently available tools for understanding population history of flying foxes. The molecular work completed is an important component of my dissertation research. I have already presented the findings at the 41st Annual North American Society for Bat Research meeting in Toronto, Canada. The talk was well received and researchers who face similar issues are excited at its potential for working in SE Asia. The role that Singapore has played as a hub was critical to my professional development. The partnerships I have formed with foreign researchers have allowed me to apply for permits in two developing countries recognized as biodiversity hotspots—Indonesia and the Philippines. I have research plans for the coming summer to visit these countries again to begin conducting fieldwork and train local researchers laboratory and analytical techniques so that they may do some of the molecular assays in the country. I have also integrated my phylogeographic interests and work with a team of virologists in Singapore, leading to a novel collaboration culminating in a long-term study of bat-borne diseases. My summer research fellowship was a great success and I look forward to continuing my work in SE Asia and returning to Singapore in the near future.