The Center for Ecological Development and Recreation (CEDAR) is an ecotourism site comprised of natural and human-modified ecosystems in Bukidnon, Philippines. With very little existing research on the influence of human-modified ecosystems on amphibian assemblages in the Philippines, we designed this study to evaluate amphibian assemblages in CEDAR. Using a combination of transects sampling, active searching, and auditory samplings, amphibian samplings were conducted at three sites: a human-modified area, a dipterocarp forest, and the Dila River System. A total of 425 individuals of 18 species from 13 genera and 7 families were documented. The family Ceratobatrachidae was the most represented group, with four species. Out of 18 species, 14 (78%) were Philippine endemics, indicating a high rate of amphibian endemism at CEDAR. In terms of IUCN conservation status, 14 out of 18 species were classified as Least Concern and two as Near Threatened, while two have undetermined conservation status. The Shannon-Weiner and Gini-Simpsons Diversity values revealed that the Human-modified area had the highest diversity compared to the Dila River System and dipterocarp forest. Surprisingly, the human-modified area in CEDAR was found to be the habitat of many anuran species, in particular, a number of generalist species, whilst some specialist species were restricted to natural habitats like the dipterocarp forest and Dila River System. The high amphibian diversity in the human-modified area requires further field studies; hence, additional amphibian samplings are recommended. Long-term wildlife evaluation and monitoring should be carried-out in CEDAR to facilitate the conservation of amphibian populations and their natural habitats in this area.