Considered as one of the most significant emerging foodborne zoonosis, we have investigated molecular mechanisms of host-parasite relationship in anisakiasis. We performed experimental infections of an accidental, rat Rattus norvegicus, and a paratenic, seabass Dicentrarchus labrax, hosts with Anisakis pegreffii L3 larvae. Transcriptomes of larvae in active penetration of rat and seabass mucosea (migrating) were analyzed and compared to larvae that were not able to engage in host tissue penetration (non-migrating). Primary experimental question was to delineate signatures of gene expression crucial for the process of host infection, as well as to see what is different when larvae encounter an evolutionary distant host, such as a rat or human. During the experiment, larvae showed no synchronized behavior in respect to specific time post-infection and were found at different migratory stages at all sampling points, although the incidence of non-migratory larvae has decreased with increasing time post-infection. In rat, an exacerbated local pro-inflammatory reaction was observed, favoring development of the Th17-type response. In contrast, the infection in seabass adopted inconspicuous character with rapid larvae clearance rate. Hence, we were not able to collect seabass tissue samples that would allow us to analyze molecular signatures in a paratenic host as well.