This study, conducted from July to November 2009, aimed to explore the diversity of large aquatic and terrestrial organisms found in microhabitats along the Jalaur River System on Panay Island, Philippines. We adopted a purposive sampling approach using several collection techniques appropriate to particular taxa or group of taxa. These include the netting method for birds and bats, cruising and transect methods for herpetofauna, gill-net fishing for aquatic vertebrates and quadrat method for macro- invertebrates. Data were analyzed for species richness (S) and relative abundance, and for fish, catch per unit effort (CPUE) and income per unit effort (IPUE). Three areas, representing the upper, middle, and lower portions of the river, served as the sampling sites. The results of the study show that there are at least 106 species of terrestrial vertebrates and about 71 species of aquatic vertebrates and macro-invertebrates in the area. These include 22 endemic species of terrestrial vertebrates, a new Philippine record of the goby Trypauchenopsis intermedia and an undescribed goby of the genus Rhinogobius. Of the 51 species of fish observed in the area, 36 species (70.59%) are known to inhabit marine and brackish water habitats, while 14 species (27.45%) inhabit freshwater. Only one catadromous species of fish, Anguilla marmorata, was observed in the area. The study also identified nine exotic species of fish and two species of freshwater mollusks are harvested in the area. The terrestrial vertebrate species diversity appears to be depauperate....