Phytoplankton availability is one of the most important biotic factors affecting the successful culture of Nile tilapia (Oreochromis niloticus, Linnaeus) in semi-intensive ponds. The present study investigated phytoplankton composition, abundance and food selectivity in Nile tilapia Oreochromis niloticus (Linnaeus, 1758) reared in monoculture and polyculture system with African sharptooth catfish Clarias gariepinus (Burchell 1822) in earthen ponds. Water samples and stomachs of 144 O. niloticus were collected from respective pond systems for examination of phytoplankton composition and abundance. The obtained phytoplankton species in water and stomachs were used to determine food selectivity of O. niloticus. The results showed significantly higher Chlorophyceae in polyculture than monoculture ponds. The gut contents of O. niloticus from both systems were mainly composed of Bacillariophyceae, Euglenophyceae and Cyanophyceae and detritus and insect remains. Bacillariophyceae, detritus and insect remains were selected as food by O. niloticus cultured in both systems. Findings from this study show that, under monoculture and polyculture pond systems, O. niloticus exhibit selective feeding consuming more Bacillariophyceae, detritus and insect remains.The results suggest that fish farmers can practice either monoculture or polyculture of O. niloticus without affecting its food selectivity.The Inter-University Council for East Africa (IUCEA) through Lake Victoria Research Initiative (VicRes)