Three independent Horizon 2020 projects are prioritising a common task of solving diagnostic issues using different approaches and strategies. PerformFISH focuses its research objectives on diagnostic methods, MedAID has prepared a diagnostic manual for the most devastating fish diseases of the Mediterranean and ParaFishControl has prepared a diagnostic manual on parasitic diseases of European aquaculture species. Currently, the projects are investing large collaborative efforts to reinforce their tasks and to deliver mutual and cutting-edge material on the subject. Nevertheless, further efforts for the harmonisation, standardisation and validation of diagnostic methods for infectious diseases in Mediterranean aquaculture are needed, involving as many relevant stakeholders and experts as possible. The main goal of the workshop (WS) 'Bottlenecks in diagnostics of Mediterranean fish diseases', organised during the 19th International EAFP conference on Diseases of Fish and Shellfish, was to present results already obtained from the projects and discuss the bottlenecks in diagnostic procedures of target groups of pathogens. The WS provided an ideal environment and opportunity to exchange and discuss experiences and data with international experts in the diagnostic field attending the conference. Interactive discussions on diagnostics for a specific group of pathogens have resulted in highlighting new initiatives needed in the management of diseases in Mediterranean aquaculture. Furthermore, the WS emphasised a need for the establishment of this strong interactive network which will collaborate to receive, collect, compile and analyse all information gathered from different parts of the region.