The European eel, Anguilla anguilla, is considered an endangered species that is under pressure for many reasons. Among others, the introduced parasite Anguillicola crassus is thought to play an important role in the decline of eel populations. These nematodes have been shown to negatively affect many fitness-related traits in eels, e.g., growth, osmoregulation, and stress tolerance. Nevertheless, there has been little work on the way in which the host–parasite interaction influences the molecular regulation of these key physiological processes. We experimentally analyzed the effect of this nematode on the expression of genes involved in the physiology of European eels during their continental life. Included are genes that are implicated in the eel's somatic growth (insulin-like growth factor 1 and thyroid hormone receptor β), osmoregulation (Na+/K+-ATPase β1 and aquaporin 3), and hematopoiesis (hemoglobin α-chain). Our results showed the absence of an effect on genes involved in fish growth; the parasite may, however, have an effect on osmoregulation and hematopoiesis. We also noted a differential impact of male and female parasites on the expression of some genes, perhaps owing to the sexual dimorphism in body size of the parasite.