Lepeophtheirus salmonis is a common parasite of salmonid fish and has a significant economic impact on Atlantic salmon (Salmo salar) fish farms. Over time L. salmonis has developed resistance to a number of chemotherapeutants, making the discovery of new treatments important to maintain a profitable farming industry. Determining processes in both L. salmonis and Atlantic salmon important to host selection and colonization may provide new targets for treatment development. During a two week cohabitation of L. salmonis infected and uninfected Atlantic salmon, we were able to collect information on the ability of L. salmonis to switch hosts, and preference for infected or uninfected fish. Whole L. salmonis and Atlantic salmon tissues were collected at 2 and 14 days post cohabitation to determine if differential gene expression was occurring during this process. At 2 days post cohabitation there was no significant difference in the number of male lice on the initially infected and uninfected fish. Eight L. salmonis genes putatively associated with various facets of lice survival (CYP18 A1-like, cytochrome p450 Isoform 1-like protein, glycene receptor α-2-like, leukocyte receptor cluster member 9-like, nicotinic acetylcholine receptor subunit-like, tissue plasminogen activator precursor-like, peroxinectin-like, and Trypsin-1) were analysed in both adult male and female lice, as well as five genes indicating immune status in Atlantic salmon. Comparisons were made to look for differential gene regulation as well as correlation between expression of L. salmonis genes and Atlantic salmon genes. Only MMP9 expression in salmon spleen was differentially regulated during the study period, however, correlations between the expression of several louse and salmon genes were found. Notably, the expression of a peroxinectin-like gene in male and female L. salmonis was correlated with the expression of IL-1, IL-12, IgT and matrix metalloproteinase 9 intermittently in salmon. This paper provides new insight into the interactions between L. salmonis and S. salar during infection.