Animal health and welfare are issues of high research priority for European aquaculture. In particular, improving animal welfare whilst reducing the use of veterinary drugs are current research priorities in line with minimizing the environmental impact of the industry. Preventing, or reducing the impact of disease is of prime importance for producers, researchers and stakeholders. In addition, public awareness of aquatic animal health and welfare leads to the increased attention of policy-makers, scientific community and the consumers into new methods for disease prevention. The IGNITION project aims to unveil new knowledge regarding animal welfare in the context of climate change and propose new tools to mitigate the adverse effects of stress. An improvement in animal welfare will translate in higher-quality farmed animals thus improving farming productivity and sustainability performance. Through IGNITION it is expected to provide new knowledge through genotyping and molecular phenotyping techniques to develop future breeding strategies for fish and shellfish. New innovative tools regarding immunization in fish will also be provided, aiming at improving fish welfare and targeting early life stages. Animal feeds will be formulated to include bioactive compounds extracted from halophytes through a novel upstream cascade salt removal. Special emphasis will be given to the study and discovery of new non-invasive biomarkers of health and welfare, which will in turn allow the development of biosensors and disease prediction through machine learning approaches. The tools developed in IGNITION will be able to avoid the colonization and spread of pathogenic microorganisms, including multi-resistant microorganisms, among farmed animals and the subsequent spread to humans through the food chain.