Organisms release and detect molecules for defense, reproduction, feeding strategies and finding suitable habitats. For some migratory species, homing behavior could be related to the recognition of their home chemical fingerprint made of an assemblage of molecules from their habitat. In the marine realm, the functioning of ecosystems such as underwater caves largely depends on trophic interactions between the caves and the outside environment. A key feature of these interactions relies on the circadian migration of small crustaceans (Mysida) from the cave habitat to the open sea. Recently, it has been hypothesized that these migrations could involve chemical mediation. Behavioral experiments using a two-choice system have shown that cave mysids significantly detect cave seawater rather than a control water from the open sea. Here, we used the same experimental system to investigate habitat recognition by two populations of the cave mysid Hemimysis margalefi . Both populations were submitted to a choice between three distinct cave seawaters vs. a control seawater. Additionally, experiments tested the water preference of a non-cave mysid species ( Leptomysis sp.) between control and cave seawaters. To evaluate whether the choice of mysids was influenced by chemical cues from conspecifics, a complementary experiment on H. margalefi was conducted. Results demonstrated that each studied mysids population significantly recognizes the water of its own home habitat, and that this behavior is not influenced by the occurrence of H. margalefi ’s exudates. Mass spectrometry-based metabolomic analyses revealed that each cave seawater had a specific chemical fingerprint with only a few reproducibly detected signals belonging to different chemical classes: peptides, alkaloids, fatty acids, steroids but also inorganic molecules. Organic pollutants have also been reproducibly detected. Among the detected compounds, one oxylipin derivative and one peptide could be considered as chemical markers of the cave ecosystem. Therefore, we postulate that the chemical seascape of each cave participates to mysid circadian migrations which are analogous to a daily-based homing behavior.