Aquaculture in Europe has experienced significant growth in recent decades, driven by rising demand for sustainable production and strong policy frameworks promoting environmentally responsible aquaculture practices. Biomarkers, defined as measurable biological indicators reflecting physiological, biochemical, or molecular responses to environmental and biological stressors, have greatly expanded their use in aquaculture applications. In this regard, biomarker-based approaches are increasingly applied in multiple areas of aquaculture, including health and disease monitoring, welfare as-sessment, environmental toxicology, reproductive biology, population management, and the optimization of cryopreservation protocols. This review provides a compre-hensive overview of current biomarker applications in European aquaculture, highlig-hting recent technological advances, methodological challenges, and emerging rese-arch directions. By synthesizing current knowledge and identifying future research priorities, this review aims to contribute to the development of biomarker-driven mo-nitoring strategies that enhance the resilience, efficiency, and sustainability of aqua-culture in Europe.