The presence of Toxoplasma gondii in shellfish has been reported across diverse geographical regions worldwide. While attention to shellfish-borne disease has largely focused on bacterial and viral pathogens, protozoan parasites including T. gondii have been recognized as foodborne pathogens that are likely underestimated as causes of illness through shellfish consumption. Furthermore, T. gondii can infect essentially all warm-blooded animals, which can result in severe morbidity and mortality in marine mammals worldwide. To date, detection methods have focused on parasite DNA, which does not inform public health and veterinary professionals about the true risk to susceptible hosts including people and wildlife. In this study, the persistence of viable T. gondii oocysts contaminating Pacific oysters (Crassostrea gigas) was assessed by quantifying the concentrations of mRNA in oysters following systematic spiking and a subsequent depuration period. To determine parasite persistence, oysters were exposed to viable T. gondii oocysts for 24 hours and then transferred into clean depuration beakers. Oysters (whole tissue) and feces/pseudofeces in water were collected at specific time points for up to 70 days. Samples were analyzed using multiplex nested polymerase chain reaction (PCR) for DNA detection and reverse transcription quantitative PCR (RT qPCR) for mRNA quantification. Our results suggest that DNA can be detected after viable parasites, as measured by mRNA, are no longer present in shellfish, providing important implications for surveillance approaches in shellfish that serve as an important seafood commodity to people as well as prey for marine wildlife.