Bats display indispensable role in the balance of the ecosystem, from pollinating flowers and eating pest to dispersing seeds of plant species that depend entirely on bats for distribution. Bats are present in almost all habitats ranging from seaside, caves, mountains, and rivers. Clarin river is one of the freshwater bodies draining from the biodiverse Mt. Malindang that hosts a large number of flora and fauna. Riparian fauna along Clarin River is not yet assessed which is the main objective of this study. Bat fauna along the upstream, middle stream and downstream of Clarin river was assessed through mist netting to provide baseline data on the species composition and distribution of bats in the area. Ten species of bats were documented in the area of which four are endemic. The highest relative abundance was observed in upstream with a value of 39.38% and the highest species diversity was recorded in the midstream with diversity index of H’ = 1.748. The results of the study may provide baseline data on the species composition and distribution of bats in the area that can be used by the local government and other agencies in conserving bats.