With the development of high throughput sequencing techniques and dedicated bioinformatics tools, molecular epidemiology has experienced a spectacular boom in recent years and has demonstrated its usefulness in human health for the early detection of emergencies and the understanding of transmission and circulation dynamics of many infectious diseases. Aquaculture is a sector particularly sensitive to infections where flocks are regularly subjected to epizootics causing considerable ecological and economic damage. Currently, the sector lacks methods for early detection, prevention and control of diseases. To address this need, we have developed a tool and methodology to accurately and rapidly identify pathogens that could cause mortality in livestock. As a proof of concept, the SEA-MONITOR project has provided a concrete solution for real-time monitoring of marine mollusc pathogens to significantly improve their prevention and control. The concept is based on the development of a suitcase containing all the laboratory equipment necessary for genomic diagnosis. More precisely, this mini-laboratory is based on the use of Oxford Nanopore Technologies (ONT) portable sequencing technology, which allows to obtain high quality genomic sequences in near-real time. The solution proposed also includes the development of an analysis pipeline allowing the transfer of raw sequencing data to an adhoc calculation server and the automatic analysis of these data to quickly provide an accurate and complete diagnostic report to users. Tests performed in laboratory as well as in the field by our partners have enabled the identification and sequencing of viral and bacterial pathogen genomes within a few days. Results of the SEA-MONITOR project have demonstrated that genomic monitoring and diagnosis represent a promising opportunity for a better management of marine mollusc diseases.