Large cichlids of the genera Oreochromis, Tilapia, Serranochromis and Sargochromis are the backbone of the gillnet fishery of the Zambezi River, but Oreochromis spp. is currently over-exploited and at risk of local extinction. As a result, the Sikunga Fish Protected Area was established in 2012 to restore a decline in fish stocks of the Zambezi River, but its efficiency has never been assessed. The aim of this study was to compare fish assemblages, abundance and mean sizes between a fish protected area (Sikunga FPA) and nonprotected areas; the Sikunga Buffer Zone and the Lisikili Fished Area on the Zambezi River. Monthly gillnet surveys, using commercial gillnets, were conducted from July to December 2020. Overall catch rate (CPUE) by weight of all species differed significantly among the sampling sites (Kruskal–Wallis H-test, range χ²(2) = −27.95, p = 0.0001). The highest CPUE was recorded at Sikunga Fish Protected Area (2.85 kg/set ± 0.42 (SE)), followed by the Sikunga Buffer Zone (0.93 kg/set ± 0.16 (SE)) and the Lisikili Fished Area (0.61 kg/set ± 0.14 (SE)). Further analyses showed that the mean sizes of O. andersonii, Coptodon rendalli, Serranochromis and macrocephalus were significantly larger at the Sikunga Fish Protected Area than at the Lisikili Fished Area. A particularly interesting observation pertains to a lack of variation in catch rates of Serranochromis macrocephalus and mean sizes of Clarias gariepinus between the protected and nonprotected areas, signifying that fish protected areas can be species-specific, and not all species in a water body will respond positively to protection. The overall results of this study support the innovation of fish protected areas as a fundamental tool in attaining sustainable management of fishery resources in inland waters of Namibia and other developing countries. Keywords: co- management, CPUE, Sikunga Buffer Zone, Sikunga FPA, species diversity, Zambezi River.