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The Ecosystem Approach to Fisheries Management agitates for provision of Marine Protected Areas (MPAs) which seem to be effective in developed countries. However, efforts to control artisanal fisheries through protection have not been adequately assessed. The Uganda portion of Lake Edward, Kazinga channel and half of Lake George are located in Queen Elizabeth National Park, controlled and managed by the Uganda Wild Life Authority (UWA). Three of the seven recognised landing sites on Lake George occur outside the park, and by proxy are unprotected. The objective of this study was to compare fishing efforts, gears and fishery yield of the protected and unprotected lake areas and landing sites of Uganda during 2011 and 2013. Fishing effort data sets were generated through periodic census of fishing inputs, in addition to the yield. Of the total annual fish production (9,200 metric tonnes) from the Edward-George system on the Uganda portion, protected areas contributed 87% and were markedly higher than the unprotected area (13%). The number of illegal gillnets in the protected area increased by 88% relative to 12% in the unprotected area, over the same period. The principle of MPAs in conservation in artisanal fisheries may not be effective and achievable in these regions.