Fasciolosis and dicrocoeliosis are severe parasitic infections that result in substantial economic damages to livestock farming globally as a consequence of reduced productivity and viscera condemnation. Molecular tests such as polymerase chain reaction (PCR) can detect Fasciola hepatica and Dicrocoelium dendriticum DNA with high sensitivity and specificity. In this study, we aimed to assess the presence of F. hepatica and D. dendriticum by PCR-based techniques in 400 small ruminant bile samples retrieved from central Portugal. Additionally, we conducted genetic characterisation of F. hepatica and D. dendriticum in these samples. Only one of the 400 bile samples (0.25%; 95% confidence interval [CI]: 0.01–1.39) examined by PCR tested positive for F. hepatica, and two samples (0.50%, 95% CI: 0.06–1.79) tested positive for D. dendriticum. Our findings indicate a low prevalence of F. hepatica and D. dendriticum in Portuguese small ruminants, underscoring the need to investigatefactors leading to meat rejection in slaughterhouses. Implementing effective parasite control measures is crucial to minimise economic losses and improve food safety. Addressing these infections and deploying targeted control strategies can enhance livestock production sustainability and ensure safe, high-quality meat products for consumers.