Three new cestode species are described from the crocodile shark (Pseudocarcharias kamoharai) in Ecuador. All three were examined with light and scanning electron microscopy. The unique combination of morphological features in one of the new species prompted formal investigation of the non-monophyly of Paraorygmatobothrium relative to the morphologically similar genera Doliobothrium, Guidus, Marsupiobothrium, Nandocestus, Orectolobicestus, Ruhnkecestus and Scyphophyllidium. Sequence data generated for part of the 28S rDNA gene were subjected to maximum likelihood (ML) analysis. The resulting tree led to the synonymization of six of these seven genera with Scyphophyllidium, and transfer of their species to the latter genus. With the new species, the number of described members of Scyphophyllidium is now 45. The diagnosis of Scyphophyllidium is revised to accommodate these species. In addition, to expedite future descriptions, eight categories of Scyphophyllidium species are circumscribed, based largely on bothridial features. Scyphophyllidium timvickiorum n. sp. is a category 1 species. Beyond being the smallest category 1 species, it bears, rather than lacks, apical suckers and lacks, rather than bears, strobilar scutes. The two other new species are members of Clistobothrium. Clistobothrium amyae n. sp. differs from its congeners in bothridial shape, elongate cephalic peduncle and tiny size. Clistobothrium gabywalterorum n. sp. differs from the two of its congeners that also possess foliose bothridia in overall size and testis number. Despite their substantial morphological differences, the ML tree indicates they are sister taxa. Both are unique among their congeners in possessing cephalic peduncle spinitriches. The diagnosis of Clistobothrium is revised accordingly.