Objective Aquaculture is a critically important part of the rural agricultural economy in Bangladesh, directly and indirectly supporting the livelihoods of millions, providing a source of dietary protein for many more, and generating export income second only to the garment industry. The routine, intermittent and unregulated utilisation of antibiotics and other selective chemicals generates risks to animal and human health through selection for AMR. We need to better understand these potential risks and develop improved AMU and AMR management systems. Methods We undertook a range coordinated activities, including stakeholder-partnered scientific research and workshops, semi-structured interviews on the farmer practices driving the use of antibiotics in different parts of the sector, training provision in disease diagnosis and treatment, bacterial diagnostics and antibiotic susceptibility testing, and the development and implementation of a pilot wet market AMR surveillance system in Bangladesh. Results We demonstrate that the heterogeneous nature of the aquaculture industry in Bangladesh profoundly affect how, and where, antimicrobials are used in the various parts of the production system. For instance, antimicrobial use in freshwater prawns and tiger shrimp destined for export markets differs from AMU in finfish (pangasius and tilapia) reared for domestic consumption. We also demonstrate how communities of practice can be established across this diverse sector and how research outputs and training opportunities can be efficiently taken up by the target audiences. Conclusions Tackling the threat of AMR requires a truly cross-sectorial, fully integrated approach, involving partners from across industry, academia and government. Meaningful change, can only be achieved over sustained timescales with full engagement of all the stakeholders, and with clearly defined and agreed mission objectives.