The uplift of the Panamanian isthmus in the Pliocene caused the termination of gene flow among members of many ancestral populations of marine lineages leading the diversification of geminate species confined to opposite sides of Central America. This palaeogeographical event has been evoked to explain the diversification of few lineages of batoids with trans-isthmian distribution. As such, there is the expectation that this vicariance event also affected lineages of parasites associated with them. Our study suggests that this event can explain the diversification of Parachristianella Dollfus, 1946 (Trypanorhyncha : Eutetrarhynchidae) in the Caribbean Sea and tropical eastern Pacific Ocean. We provide molecular, morphological and biogeographical evidence to recognise five lineages within this genus inhabiting the coastal waters of Panama, including P. parva Campbell & Beveridge, 2007 and four new species: P. mendozai, sp. nov., P. kuchtai, sp. nov., P. campbelli, sp. nov. and P. soldanovae, sp. nov. These species can be diagnosed by unambiguous sets of molecular characters. The morphological cohesiveness of sister species, which most likely diverged from around 3 million years ago through the uplift of the Panamanian isthmus, suggests that the traditional emphasis on the tentacular armature to circumscribe species within trypanorhynchs might underestimate the diversity of recently diverged lineages.