An intensive anuran survey was conducted using cruising and mark-release-recapture methods for a total of 168 man-hours on April 28 to 30, 2017 at Barangay Calaitan, Andanan Watershed, Bayugan, Agusan del Sur. The study aimed to record and statistically define anuran species populations in three types of water systems (streams and creeks, the river of Calaitan, and Lake Danao) with notes on habitat association; and to provide additional baseline data to the existing records of Mindanao amphibian fauna. A total of 141 individuals of anurans belonging to eleven species and seven families were recorded, of which 73% were Philippine endemics, and 36% were Mindanao faunal endemics. Only Megophrys stejnegeri was regarded as vulnerable and Limnonectes magnus as near threatened by IUCN 2016. The diversity of anurans was highest in Lake Danao ( H’ = 1.69, S = 7, n = 54) followed by anuran diversity in the Calaitan river ( H’ = 1.40, S = 7, n = 42), and in the streams and creeks ( H’ = 1.30, S = 6, n = 43), with no significant difference ( p = 0.9167). However, anuran species composition differd between sites ( p = 0.038). Microhabitat overlap was observed in anuran preferences since many of the encountered species utilized both aquatic and terrestrial microhabitats. An ordination biplot (canonical correspondence analysis) revealed two habitat types, wherein M. stejnegeri and Platymantis dorsalis were associated with humidity, canopy cover, moss percentage, rock percentage and distance to disturbance. Philippine endemic species were closely associated with forest habitats. However, the presence of forest clearings for cultivation was an indicator of forest degradation. The high degree of endemism and presence of threatened taxa indicated a need for conservation intervention since anthropogenic activities were evident even in highlands of the protected area.