The present study reported parasites and its histopathological effects on the tissue of the popular seafood clam Paphia undulata. Some parasites were found to have several effects on shellfish aquaculture production. Samples of clams were collected from Damietta shore, Egypt. Histopathological examination was conducted on the gills, gonads, and intestine of clams. Two types of parasites were detected in the infected clams (protozoans and nematodes). The identification of Protozoa was confirmed by using the electron microscope. This study revealed that 51% of P. undulata were infected with parasites. The highest infection was noticed in the clam size ranged from 2.1 to 4 cm. This infection declined with the larger clams. The current study proved that there was a negative association between the prevalence of parasites and clam size. Histopathological effects of parasites on the clam gills, gonads, and intestine were detected. Parasites not only affect clams but may also be transmitted to consumers after eating undercooked shellfish. So, this study warns against eating raw seafood as it is considered a vehicle for the transmission of human parasites.