Population size structure and maximum size of managed sportfish populations are dictated by abiotic, biotic, ecosystem, and anthropogenic influences. In their native ranges of northern Wisconsin, muskellunge (Esox masquinongy ) and cisco (Coregonus artedi ) are co‐adapted cool‐ and cold‐water species where cisco presence may influence population size structure and maximum size of muskellunge. We tested whether muskellunge size structure indices (length‐frequency distributions, proportional size distribution), mean length, and mean maximum length of muskellunge differed when cisco were present or absent in Ceded Territory of Wisconsin (CTWI) lakes during 2015–2018. Cisco presence had a positive influence on size structure and mean length of individual muskellunge within populations. In contrast, cisco presence had no influence on the mean maximum length of muskellunge observed in CTWI populations suggesting that other factors may be better predictors of this metric than cisco presence. In cisco lakes, mean muskellunge length was negatively correlated with mean cisco length suggesting that gape limitation may be a factor influencing population size structure and individual growth rates. Therefore, cisco populations with primarily large individuals may be unavailable to muskellunge as forage. Our results suggest that cisco are an important forage species for some aspects of muskellunge population ecology; however, other factors may also contribute to muskellunge population size structure and maximum size outcomes. As such, conservation of remaining cisco populations in Wisconsin is critical because they influence muskellunge population ecology in lakes where the species coexist. Future research is needed to better understand the interactions of cisco, abiotic and biotic factors, and anthropogenic influences on muskellunge growth dynamics.