Lake trout refuges in the Apostle Islands region of Lake Superior are analogous to the concept of marine protected areas. These refuges, established specifically for lake trout (Salvelinus namaycush) and closed to most forms of recreational and commercial fishing, were implicated as one of several management actions leading to successful rehabilitation of Lake Superior lake trout. To investigate the potential significance of Gull Island Shoal and Devils Island Shoal refuges for populations of not only lake trout but also other fish species, relative abundances of lake trout, lake whitefish (Coregonus clupeaformis), and cisco (Coregonus artedi) were compared between areas sampled inside versus outside of refuge boundaries. During 1982–2010, lake trout relative abundance was higher and increased faster inside the refuges, where lake trout fishing was prohibited, than outside the refuges. Over the same period, lake whitefish relative abundance increased faster inside than outside the refuges. Both evaluations provided clear evidence that refuges protected these species. In contrast, trends in relative abundance of cisco, a prey item of lake trout, did not differ significantly between areas inside and outside the refuges. This result did not suggest indirect or cascading refuge effects due to changes in predator levels. Overall, this study highlights the potential of species-specific refuges to benefit other fish species beyond those that were the refuges' original target. Improved understanding of refuge effects on multiple species of Great Lakes fishes can be valuable for developing rationales for refuge establishment and predicting associated fish community-level effects.