Chimaeras, or ratfishes, are the only extant group of holocephalan fishes and are the sole host group of gyrocotylidean cestodes, which represent a sister group of the true tapeworms (Eucestoda). These unique, non-segmented cestodes have been known since the 1850s and multiple species and genera have been erected despite a general agreement that the delineation of species on the basis of morphology is effectively impossible. Thus in the absence of molecular studies, the validity of gyrocotylid taxa and their specific host associations remain highly speculative. Here we report the presence of Gyrocotyle species from rarely-caught deep-sea chimaera species collected in the northeastern Atlantic, and describe two new species: G. haffii n. sp. from the bent-nose chimaera, Harriota raleighana Goode & Bean and G. discoveryi n. sp. from the large-eyed rabbit fish, Hydrolagus mirabilis (Collett). Nuclear ribosomal sequence data were generated for individual parasites taken from different host species collected on different dates and from different localities and were combined with sequences previously published. Phylogenetic analyses support the recognition of independent lineages and clusters, indicative of species, but were indecisive in recovering the root of the ingroup in analyses including eucestode, outgroup taxa. The molecular data reveal variation not reflected in their morphology and point to a complex picture of genetic divergences shaped by both isolation and migration in deep-sea environments.