Identifying marine trematode parasites in host tissue can be complicated when there is limited morphological differentiation between species infecting the same host species. This poses a challenge for regular surveys of the parasite communities in species of socio-economic and ecological importance. Our study focused on identifying digenean trematode species infecting the marine bivalve Cerastoderma edule across Europe by comparing morphological and molecular species identification methods. Cockles were sampled from ten locations to observe the trematode parasites under a stereomicroscope (morphological identification) and to isolate individuals for phylogenetic analyses using two gene markers, the small sub-unit ribosomal (18S) RNA gene (SSU rDNA) and the mitochondrial cytochrome c oxidase subunit 1 (cox1). For the first time, we compared both morphological identification and phylogenetic analyses for each of the 13 originally identified species. First, we identified a group of five species for which morphological identification matched molecular results (Bucephalus minimus, Monorchis parvus, Renicola parvicaudatus, Psilostomum brevicolle, Himasthla interrupta). Second, we identified a group of six species for which molecular results revealed either misidentifications or cryptic diversity (Gymnophallus choledochus, Diphterostomum brusinae, Curtuteria arguinae, Himasthla quissetensis, H. elongata, H. continua). Third, our analyses showed that all sequences of two expected species, Gymnophallus minutus and G. fossarum, matched between the two, strongly suggesting that only G. minutus is present in the studied area. Our study clearly demonstrates that molecular tools are necessary to validate the trematode species composition. However, with 17 distinct genetic lineages detected, some of which are not fully identified, future studies are needed to clarify the identity and status (regular vs. accidental infection) of some of these cryptic trematode species.