Trypanorhynch tapeworms are marine heteroxenous parasites, involving sharks and rays as definitive hosts, invertebrates (i.e. crustaceans) as first intermediate hosts, and various teleost fishes as intermediate/paratenic ones. The massive presence of Trypanorhyncha larval forms in the flesh or body cavity of the fish hosts reduces their market value, making them unappealing to consumers, or causing discards of fish products. The identification of merocercoids (N = 100) of Molicola uncinatus and plerocercoids (N = 46) of Hepatoxylon trichiuri parasitizing the silver scabbardfish, Lepidopus caudatus, from the Central Mediterranean Sea (off Malta coast), was obtained, for the first time, by using sequences analysis of the complete small subunit (ssrDNA) and the partial large subunit (lsrDNA) ribosomal RNA gene loci. The Bayesian Inference from the concatenated sequences obtained at the two gene loci showed that the individuals of M. uncinatus and H. trichiuri clustered, respectively, in two well distinct and supported phylogenetic lineages, corresponding to the two cestode species. High prevalence (P) and mean abundance (MA) values were observed in the infection with merocercoids of M. uncinatus (P = 100%, A = 28.81), with the ventral musculature of the silver scabbardfish as the most parasitized site. Plerocercoids of H. trichiuri were found to infect only the mesenteries, attached to various fish tissues, with a mean abundance rate of 1.28. Even if harmless to humans, a heavy parasitic load with larval stages of Trypanorhyncha, particularly in the edible part of the silver scabbardfish (as here reported for merocercoids of M. uncinatus), can compromise the appearance of the fish-food, making it repugnant and unappealing for the final consumer. It has been also discussed that when managing the risk related to parasites affecting the fish quality and safety of fisheries products, the fishing ground where the life cycle of those parasites takes place should be also taken into account, as it would include the ecological drivers of the infection with those parasites. This wider ecological approach would be of help to the Food Business Operators (FBOs), gathering knowledge useful to manage fisheries in a wide "One-Health" perspective, aware of sustainability, quality and consumer safety aspects of seafood production.