The disease saprolegniosis is a major problem in the aquaculture industry with losses of up to 10% of fish caused by the oomycete pathogen Saprolegnia parasitica. As with all pathogens new genetic variations emerge within a species. Indeed, we isolated several distinct S. parasitica phylotypes (strains) from 14 Scottish fish farms in collaboration with our aquaculture partners in a recent study, and we have now established that there are six distinct phylotypes of S. parasitica with different levels of heterozygosity, that can be found across Europe. But we also found that although there were 5 different phylotypes present in the Scottish fish farms, essentially only one particular S. parasitica phylotype was infecting Atlantic salmon. The phylotype of a S. parasitica isolate is defined by its internal transcribed spacer sequence (ITS). The ITS sequence of the six phylotypes are very similar (i.e. one or two base pair differences), indicative of the extent of whole genome similarities of these S. parasitica phylotypes. We therefore propose to exploit this to determine what is unique in the whole genome sequence of the pathogenic strains in comparison to the non-pathogenic strains. We have already recently performed Illumina sequencing of a total of 41 Saprolegnia isolates. These genomes cover the six phylotypes from S. parasitica, as well as isolates from Saprolegnia australis, Saprolegnia diclina and Saprolegnia ferax, all found in Scottish aquaculture sites. This resource is now available to search for unique target genes that are distinct for the individual phylotypes, in particular for the pathogenic phylotype. Therefore, our main objective is to perform a comparative analysis of the whole genome sequences of all phylotypes found in the farms and determine what unique genes the pathogenic isolates have that can be used to develop a quantitative detection test initially via a PCR based test but ultimately with a more-preferred handheld antigen testing kit. Furthermore, the current approach to develop and use a quantification method that does not discriminate between the phylotypes is essentially futile because only one phylotype is relevant for the outbreaks we see in the farms. Moreover, an outbreak with Saprolegnia is usually a rapid overnight event. Thus, the development of a rapid and accurate quantitative diagnostic kit for only the pathogenic phylotype would greatly facilitate our industrial partners in making informed decisions as to treat or not to treat, based on various parameters including the spore load of the pathogenic phylotype in the water and would provide a focused and sustainable disease management approach that will ultimately reduce the use of chemicals in aquaculture.