Polydora and related genera are common pests for molluscs. Establishing differences between native species and recent invaders provides the basis for understanding the effect of parasites and has implications for resource management. P. biocipitalis has been reported as a recently introduced species to the Chilean-Peruvian coast, raising concerns about its threat to native bivalve species. In contrast, studies on the infestation of P. bioccipitalis on the surf clam Mesodesma donacium, one of the most important species for shellfisheries, suggest a long-term parasitic relationship. The present study analyses infested (i.e. blistered) fossil shells of M. donacium deposited during the Holocene and Middle Pleistocene epochs and critically reviews evidence supporting the hypothesis of the recent introduction of P. bioccipitalis to the Chilean-Peruvian coast. The blistering pattern seen on fossil and recent shells can be considered species-specific for the infestation of M donacium by P. bioccipitalis. No evidence was actually found on vectors, introduction pathways or distribution range to support the status of P. bioccipitalis as an introduced species. On the contrary, our findings point to a long-term association, at least for several hundred thousand years, between M donacium and P. bioccipitalis.