Caligus rogercresseyi is an ectoparasitic copepod that negatively affects the salmon farming industry, causing economic losses. To use phytochemicals as feed additives, or other chemicals that could elicit behavioral responses in C. rogercresseyi, the chemosensory recognition process is crucial. Therefore, to establish how C. rogercresseyi recognizes glucosinolates and their derivates isothiocyanates, a chemosensory protein (CSP) described as specific carrier of these chemicals in sea louse (CrogCSP) was identified in this study. The recombinant CSP and its selectivity against different chemical compounds was tested by fluorescence binding assays. Phylogenetic analysis revealed a close relationship among CrogCSP and other reported CSPs. Our results indicate that phenyl isothiocyanate and isophorone exhibited dissociation constants of 4.17 and 4.28 μM of Ki, respectively, indicating affinity over other chemicals, such as fatty acids and sinigrin. Structural findings suggest a unique binding site capable of accept several types of chemicals, similar to what has been reported for crystallized insect CSPs. Finally, this study lays the foundation for a deeper understanding of CSPs in crustaceans and especially in C. rogercresseyi. Likewise, the identification of chemosensory proteins could serve as the first step towards novel semiochemicals discovery to being applied in the sea louse controlling.