Bats are biological species that can be influenced by environmental changes. The nature and understanding of the adaptation and survival of bats as biological indicators of the health of the ecosystem is essential for preservation and conservation strategies. Fluctuating asymmetry (FA) are fine and random deviations from perfect symmetry of organism’s morphology. It is considered as a reliable factor for measuring developmental instability because it reflects both genetic and environmental stresses especially in endangered populations. Hypothesis assumes that FA has costs and reflects the degree of stress and quality of individuals herewith, a direct relationship between FA and developmental instability. The study determined the developmental instability via fluctuating asymmetry of Rousettus ampexicaudatus, a fruit bat. Using landmark method for shape asymmetry, anatomical and mathematical landmarks were used and analyzed using Symmetry and Asymmetry in Geometric Data (SAGE) program. Results yield highly significant FA for both populations examined (Tamboco cave & Claise cave, Bohol). However, population from claise cave in Nagtuang of loon has relatively higher FA and percentage of variation based on the Principal component Analysis (PcA). Thus, the bat population in claise cave experienced a higher degree of stress.