Objective. To determine the presence of Perkinsus sp. in the sand clam Chionista fluctifraga cultivated in an intertidal zone of the southeastern Gulf of California, using Ray's thioglycollate fluid medium staining (MFTR) and polymerase chain reaction (PCR). Material and Methods. The prevalence and parasite load of Perkinsus sp. were monthly obtained and correlated with environmental water conditions and clam biometric indicators (n = 540), from May 2018 to September 2019. Results. Presumptive hypnospores of the protozoan were detected in eight months of culture. The prevalence fluctuated from 3.3% to 13.3%, while the average parasite load ranged from 2 to 1286 hypnospores/g of tissue. The intensity of infection varied from negative to light. The prevalence and parasite load were correlated with each other (r=0.61, P˂0.05) but not with the environmental parameters, nor with the biometric indicators of the clam. The PCR test was negative for the MFTR positive cases. Conclusions. Presumptive hypnospores of Perkinsus sp. were detected in C. fluctifraga without clear indications of infection that compromised the clam health in culture. The constant monitoring of Perkinsus sp. in C. fluctifraga is highly recommended to establish possible infections.