Jellyfish have been implicitly linked to a number of fish kill events in marine-farmed finfish over recent decades. However, due to insufficient data, it is difficult to identify small hydrozoan jellyfish as the causative agents of the more common and chronic problem of gill disorders. Gill disorders (physical, pathogenic or parasitic damage to the gills) can be caused by a number of water-borne agents and are an increasing though poorly understood problem for the aquaculture industry. Hence, the first year-long monitoring programme to study hydrozoan jellyfish, other gelatinous zoo-plankton, phytoplankton and fish health was initiated at 2 aquaculture sites on the west coast of Ireland. At the southern site, 2 jellyfish species previously implicated in aquaculture fish kill events (Muggiaea atlantica and Solmaris corona) occurred at high abundances (combined density of similar to 450 jellyfish m(-3), an order of magnitude lower than during previous mass mortality events). The fish at this site exhibited clinically significant gill damage throughout the peak in jellyfish abundance. Analyses revealed a significant positive correlation between daily fish mortality and the abundance of these jellyfish but not with any other factors. At the northern site, there were low abundances of jellyfish; nevertheless, gill damage due to the protozoan parasite Trichodina sp. was observed over a shorter time period. As the European aquaculture sector experiences annual economic losses due to gill disorders, these findings raise concerns for the expected growth of the industry, especially as jellyfish populations are predicted to increase in some areas. Therefore, mitigation methods need to be developed and implemented.