Aquaculture systems are highly complex and influenced by environmental, biological, cultural, socio-economic and human behavioural factors. The growing importance of aquaculture is fuelling a transition of small-scale farming to industrial intensification in LMICs. Two interdisciplinary workshops were held in 2018, in Vietnam and Egypt. They aim to use a ‘systems-thinking’ approach to map aquaculture systems and identify potential hotspots for the emergence and selection of resistance and human exposure to antibiotics and antibiotic-resistant organisms. Both workshops were also designed to develop systems thinking and experience in mapping systems, to build collaborations and understanding of different expertise.