Over the past decade, seafood mislabeling has been increasingly documented, raising public concern over the identity, safety, and sustainability of seafood. Negative outcomes from seafood mislabeling are suspected to be substantial and pervasive as seafood is the world’s most highly traded food commodity. Here we provide empirical systems-level evidence that enabling conditions exist for seafood mislabeling in the United States (US) to lead to negative impacts on marine populations and support consumption of products from poorly managed fisheries. Using trade, production, and mislabeling data, we determine that substituted products are more likely to be imported than the product listed on the label. We also estimate that about 60% of US mislabeled apparent consumption associated with the established pairs involves products that are exclusively wild caught. We use these wild-caught pairs to explore population and management consequences of mislabeling. We find that, compared to the product on the label, substituted products come from fisheries with less healthy stocks and greater impacts of fishing on other species. Additionally, substituted products are from fisheries with less effective management and with management policies less likely to mitigate impacts of fishing on habitats and ecosystems compared with the label product. While we provide systematic evidence of environmental impacts from food fraud, our results also highlight the current challenges with production, trade, and mislabeling data, which increase the uncertainty surrounding seafood mislabeling consequences. More integrated, holistic, and collaborative approaches are needed to understand mislabeling impacts and design interventions to minimize mislabeling.