The Polichete worms of the genus Polydora are considered very destructive for oysters, excavating channels in their shell and inducing oysters to create mud blisters in response to the irritation, interfering with their physiology and ethology. The parasite also causes important economic damage for oyster farmers, as products with a high degree of infestation cannot be commercialized. The present study aims to evaluate whether two non-invasive advanced diagnostic techniques, computed tomography scans (CT) and magnetic resonance imaging (MRI), are suitable to show the alterations induced by this parasite on live Crassostrea gigas and Ostrea edulis oyster broodstocks. A CT scan is also able to identify small lesions in the shell during the first stage of infection. MRI allows for the visualization of the advanced status of the lesions when blisters occupy the inner surface of the shell and can impact the health status and the economic value of the mollusk. Both techniques resulted in satisfactory spatial resolution, and no motion artifacts were reported, thus enabling the authors to faithfully visualize in vivo the damage caused by the parasite.