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Marine protected areas have been shown to conserve aquatic resources including fish, but few studies have been conducted of protected areas in freshwater environments. This is particularly true of Lake Tanganyika, Tanzania. To better conserve the lake’s biodiversity, an understanding of the role played by protected areas in conserving fish abundance and diversity is needed. Sampling of fish and environmental parameters was performed within the Mahale Mountains National Park (MMNP) and nearby unprotected areas at depths between 5 m and 10 m. Twelve replicates of fish sampling were performed at each site using gillnets set perpendicularly to the shore. Mann-Whitney tests were performed, and the total amount of species turnover was calculated. A total of 518 individual fish from 57 species were recorded in the survey. The fish weight abundance was fivefold greater in the MMNP than in the unprotected areas. Fish abundance and diversity were higher in the MMNP than in the unprotected areas and decreased with distance from it. Our findings confirmed the importance of the protected area in conserving fish resources in Lake Tanganyika. The study provides baseline information for management of the resources and guiding future studies in the lake and other related ecosystems. Management approaches that foster awareness and engage with communities surrounding the MMNP are recommended for successful conservation of the resources in the region.