The immune response that is triggered in the skin of salmon is critical for the ability of individuals to resist infection to many bacterial and viral diseases, and to parasitisation. Some parasites, such as sea lice, can effectively suppress the immune response of host species such as Atlantic salmon, but the precise mechanisms involved are poorly understood. The mechanisms that make some species, strains and families of salmon more resistant to disease are also generally poorly understood. RNA-seq can be used to give a broad picture of how overall populations of cells in a skin sample react to infection or infestation, but bulk RNA-seq methods are unable to differentiate between the reaction of different cell types, skin layers or to compare the reaction at precise sites of infection/attachment compared to other areas in the skin. Here we describe mapping of gene expression profiles in Atlantic salmon skin using spatial transcriptomics. This technique allows us to map gene activity in two dimensions in a ~6.5mm2 section with ~10 cell resolution. We highlight how spatial transcriptomics can complement data from single-nuclei RNA-seq (which can be used to track gene activity in different cellular populations), and how these techniques can be integrated to discover functional genetic mechanisms involved in providing resistance to sea lice.