There is increasing evidence that phenotypic variation can strongly impact community structure and ecosystem functions. Alewife Alosa pseudoharengus is a planktivorous fish species that strongly impact lake ecosystems. It has previously been demonstrated that phenotypic variation related to differences in life history among landlocked and anadromous alewife populations alters the strength of interactions with other species, potentially modifying its role in the community. The migration between freshwater and marine ecosystems by anadromous alewife creates seasonal differences in alewife densities, which causes lake zooplankton communities to alternate between large-body size and higher densities in the spring, and small-body size and low densities in the summer and fall. In lakes with resident (landlocked) alewife, predation from alewife modifies the zooplankton community to having low zooplankton densities and mainly small-bodied zooplankton year-round. The strong effects of phenotypic variation in alewife on zooplankton may be important for coexisting species that rely on zooplankton as a resource. Here we use estimates of growth, and direct diet and stable isotope analyses to ask if the presence- and phenotypic variation of alewife alters the ontogenetic trajectory of young-of-the-year (YOY) largemouth bass Micropterus salmoides, which depend on zooplankton in the early life stages. We found that both the presence- and phenotypic variation of alewife affects growth, trophic position, and diet of largemouth bass. YOY largemouth bass from lakes without alewife grew faster, switched to piscivory earlier, and reached higher trophic positions than in alewife lakes. In lakes with landlocked alewife largemouth bass grew slower and obtained a lower trophic position than those in lakes with anadromous alewife. These divergences can be explained by the strong effects of alewife on zooplankton community structure. Our results demonstrate how the strong effects of phenotypic variation can propagate through natural food webs to influence important life history transitions in other species.