Bats are integral components of the environment serving an indispensable role in maintaining the health of different ecosystem ranging from forested areas up to riparian zones. Rivers and riparian areas provide an important habitat for bat fauna by providing direct valuable resources. The bat fauna along the Cagayan de Oro river had never been assessed and the current study was the first. Bat survey was conducted in different relevant locations along the river communities through mist netting designed to provide baseline ecological information and initial data on species composition and biometrics of bat species present in the Cagayan river zone. Eight bat species – five Pteropodids, two Vespertilionids and one Emballonurid – were recorded representing 15% of the bats of Mindanao faunal region and over 10% of the total Philippine bat fauna. Two species were Philippine endemics though with stable population status but are considered of conservation priority. Further studies along more complete portions of Cagayan de Oro river would likely add essential information on bat species composition and distribution in the area and would give a clearer overview regarding the bat fauna along the Cagayan de Oro river.