Evidence about the diet and the type of association, commensalistic or parasitic, of species of Balaenophilus is not conclusive. In this study, we addressed these questions based on patterns of microhabitat selection, SEM and immunohistochemistry analyses of gut contents of the two species in the genus, B. unisetus and B. umigamecolus. We also made histopathological descriptions of the sites where the latter species occurred. Heavy infections of B. unisetus were found on the baleen plates of 18 out of 20 fin whales, Balaenoptera physalus, captured off the NW coast of Spain. Gut contents were packed as food pellets that were composed mostly of baleen tissue, as indicated by both SEM and immunohistochemistry. Individuals of B. umigamecolus appeared in 43 out of 52 loggerhead sea turtles from the Western Mediterranean. In six turtles analysed in detail, copepods occurred mostly in the hinge region between limb scales and on the skin of the cloacal region; rarely under whitish skin lesions on the neck and hindlimbs. No food pellets could be found in 20 individuals examined, but two of them had pieces of tissue in the mouth that resembled turtle skin. The histopathologic analysis was also compatible with mild host reaction to the erosion of epidermis produced by B. umigamecolus. The occurrence of Balaenophilus spp. as ectoparasites of phylogenetically unrelated hosts which, however, provide similar keratin-rich habitats, might suggest that the exploitation of this food resource (an ecological novelty among crustaceans) is in the origin of these associations. This hypothesis is further supported by the record of another putative species of Balaenophilus on the skin of sirenians. © 2006 Springer-Verlag.