The surveillance and treatment of parasites are important features of preventative healthcare plans in zoological institutes. The parasite control strategies employed in temperate regions often involve prophylactic anthelmintic treatments during seasons where the burden of gastrointestinal parasites in fecal testing is high. These strategies are, however, not applicable in the tropics, where temperatures remain high throughout the year, allowing continuous parasitic development. A risk-based parasite management strategy was adopted by a tropical zoological institute. For parasite surveillance, routine fecal direct smears and magnesium sulfate flotations were performed to determine parasitic prevalence. The frequency of fecal checks for the year was determined by the frequency at which clinically relevant parasitism (fecal tests that resulted in the animal being treated) was detected during routine fecal checks in the previous year. A yearly anthelmintic drug-class rotation schedule was also implemented. The total number of fecal tests performed per year and the number of animals with clinically significant parasitic disease decreased by 30.0% (637/2126) and 46.9% (207/451), respectively, over the four-year period of the study. Anthelmintic class rotation also improved the efficacy of fenbendazole in treating Strongyloides spp. infecting the group of orangutans. This parasite control strategy is a targeted approach to managing preventative healthcare, reducing the work required to perform routine surveillance tests whilst maintaining the health of the collection of animals.