In Lake Nabugabo, Uganda, a small satellite of the equatorial Lake Victoria, approximately 50% of the indigenous fish species disappeared from the open waters subsequent to establishment of the introduced predatory Nile perch (   Lates niloticus ). However, several of these species persisted in wetland refugia. Over the past decade, Nile perch in Lake Nabugabo have been intensively fished. Herein we report a resurgence of some indigenous species in open waters. In a multiyear study, we used annual transects in inshore and offshore waters of exposed ( no wetland ) and wetland habitats to document the pattern of resurgence. In 1995, haplochromine cichlids were largely confined to inshore areas, particularly wetland ecotones, and were rare in Nile perch stomachs, as were most other indigenous species. By 2000 haplochromine cichlids were abundant in inshore and offshore areas of both exposed and wetland transects. Several indigenous noncichlids also reappeared in the main lake, including three of the four original mormyrid species. Between 1995 and 1999, there was a dramatic increase in the proportion of haplochromines in the diet of Nile perch. When haplochromines were rare ( 1995 ), Nile perch switched from an invertebrate-dominated diet to piscivory at a large size ( 30 cm total length ). In 2000, however, Nile perch were strongly piscivorous by 5–10 cm total length. The pattern of faunal loss and recovery in Lake Nabugabo demonstrates the importance of refugia in providing the seeds of resurgence and provides a model with which to understand some changes in Lake Victoria.