In this study, we compare the diet, life history characters and abundance of Nile tilapia (Oreochromis niloticus) stocks between two crater lakes in western Uganda (Lake Nyamusingiri and Lake Kyasanduka) that differ in their history of fishing pressure. Both lakes support native fish communities, but also harbour populations of introduced O. niloticus. Lake Nyamusingiri was characterized by a higher relative and absolute abundance (CPUE) of haplochromine cichlids and a lower abundance of O. niloticus than in Lake Kyasanduka. In addition, the O. niloticus population in Lake Nyamusingiri exhibited a smaller mean size and a lower relative abundance of juveniles than in Lake Kyasanduka. These differences may reflect, at least in part, heavy exploitation of O. niloticus in this lake, as compared with Lake Kyasanduka where fishing was banned in 1988. In both lakes, the maximum size and size at maturity was small relative to other larger water bodies in the region. The Nile tilapia in both lakes were primarily herbivorous; with phytoplankton dominating the diet. In general, the condition of O. niloticus in the crater lakes was low relative to other larger lakes in the region. The low catch per unit effort of O. niloticus in Lake Nyamusingiri (7.8%) relative to Lake Kyasanduka (54.9%) suggests that overexploitation of the fishery is occurring, calling for careful monitoring and management of the system.