Cumulative data from other parasites suggests that blocking of Aquaporin channels (AQPs) may provide a suitable target for the use of pharmaceuticals to control these diseases. Neoparamoeba share many similarities with other pathogens. However, there is a need to correctly identify the Neoparamoeba AQPs at the molecular level, to undertake preliminary studies to show that these AQPs can be blocked preferentially (without affecting Atlantic salmon AQPs), and to show that block of the parasite AQPs results in inhibition or death of the Neoparamoeba. Central to this work and indeed to any further AGD research is a need to develop low cost, rapid and reliable assays of salmon gill cell – Neoparamoeba interactions. These in-vitro assays would lead to real dollar savings in the search for alternative AGD treatments by providing high throughput capability to assess multiple treatment options (pharmaceuticals, vaccines, chemicals). They provide a means of investigating amoebae – gill interactions as well as differential (pathogen versus host) effects of treatments. Dr Benita Vincent at CSIRO has begun pilot development of these assay systems with good early success, however, further resources are required to see this work to fruition.