Samples of anadromous Alosa alosa (Clupeidae) (n = 163) and Alosa fallax (Clupeidae) (n = 223), caught in Western Iberian Peninsula Rivers from 2008 to 2013, were examined for buccal, branchial and internal macroparasites, which were identified using morphological and molecular methods. Alosa alosa were infected with Anisakis simplex s.s., Anisakis pegreffii, Hysterothylacium aduncum, Rhadinorhynchus pristis, Mazocraes alosae, Hemiurus appendiculatus, Ceratothoa italica and an unidentified ergasilid copepod. Ceratothoa italica represents a new host record for A. alosa. Alosa fallax were infected with A. simplex s.s., A. pegreffii, H. aduncum, H. appendiculatus, Clavellisa emarginata and an unidentified cymothoid isopod. This is the first report of C. italica, C. emarginata and M. alosae in the Iberian Peninsula. The phylogenetic positions of M. alosae, H. appendiculatus and C. emarginata were assessed using 18S and 28S ribosomal RNA (rRNA); our contributions provide a better understanding of the phylogenetic relationships within their groups. Qualitative and quantitative differences in the parasite faunas of these two shad species are consistent with different feeding strategies. The results provide information about host migration behaviour and transmission pathways through diet during the marine trophic phase of the shad's life cycle and their roles as paratenic or final hosts and transporters of parasites between seawater and freshwater environments. The zoonotic parasites A. simplex s.s. and A. pegreffii pose a risk for consumers or riverine mammals (e.g. European otter). The use of parasites as biological tags for shad stocks in Western Iberian Rivers could be a useful approach in multidisciplinary studies concerning fish stock delimitation and characterization.