How does a single gene affect the ecosystem? Although previous studies have demonstrated how a phenotype affects its environment, the ecological impacts caused by specific genetic changes are less understood. The three-spined stickleback is a good model for elucidating the links between genetics and ecology as it has diversified into multiple ecotypes in both marine and freshwater environments. We have recently revealed that the convergent evolution of thyroid stimulating hormone (TSHß2) underlies the variation in reproductive seasonality. TSHß2 exhibits a photoperiodic response in ancestral marine ecotypes, but not in multiple stream ecotypes showing extended breeding seasons. Genome editing showed the pleiotropic function of TSHß2 in gonad maturation, body growth, and brain transcriptome. To investigate the potential impacts of genetic changes in TSHß2 on the ecosystem, we analyzed foraging traits including feeding behavior, prey preference, and trophic morphology of TSHß2-knockout (KO) marine ecotypes. TSHß2-KO fish were more active but are less likely to attack than the wild type and preferred planktonic Daphnia over benthic Asellus. We confirmed that Asellus decomposes leaves, indicating TSHß2 expression could influence the entire ecosystem through the food chain. These findings are a first step in understanding how a gene can affect the ecosystem through pleiotropic functions.