Bivalves have been shown to be carriers of the human intestinal parasites Cryptosporidium parvum and Toxoplasma gondii. The goal of this study is to determine the prevalence of protozoan parasites in mollusks of New York City using a polymerase chain reaction (PCR)-based assay. Four species of mollusks, Mya arenaria, Geukensia demissa, Crassostrea virginica, and Mytilis edulis, were collected from Orchard Beach, NY in the fall of 2014, totaling 159 specimens. Each individual mollusk was dissected to harvest the digestive gland, the mantle, the gills, the foot and the siphon. The tissues were assayed for the presence of Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii DNA by using primers that target parasite-specific genes. C. parvum was found at a prevalence of 50%, 11.3%, and 1%, respectively, in Mya arenaria, G. demissa, and Mytilis edulis. C. parvum DNA was detected in all the tissues of these bivalve species, except the gills. Furthermore, G. lamblia was detected in Mya arenaria, G. demissa, Crassostrea virginica and Mytilis edulis at a prevalence of 37.5%, 4.5%, 60%, and 20.6%, respectively, while T. gondii DNA was not detected.