Blastocystis, a common intestinal protist found in humans andanimals, presents significant challenges in epidemiology dueto its diverse host range and unclear pathogenicity. From a “One Health” perspective, which integrates human, animal, and environmental health, understanding Blastocystis is crucial for understanding transmission dynamics and host-protist interactions, thereby clarifying the clinical and publichealth significance. Blastocystis is globally distributed, with prevalence ratesvarying by region, often higher in developing areas. Currently, at least 42 genetic subtypes (STs) exist and ST1 toST4 are predominantly found in humans, while others infect a range of animals and rarely humans. To improve of the knowledge for Blastocystis epidemiologyis needed a One Health approach, involving surveillanceacross human, animal, and environmental components. New strategies for focusing on the molecular epidemiology of Blastocystis are essential, especially for detecting Blastocystissubtypes and intrasubtype variations, providing an understanding of the characteristics of Blastocystis. Developing and disseminating strategies to determine themolecular epidemiology of Blastocystis within a One Healthperspective will enable the identification of the distribution of subtypes and intrasubtype variations across differentgeographic regions, thereby clarifying the transmissiondynamics and zoonotic potential, monitoring the reservoirs of this protist. In providing the necessary data for Blastocystis epidemiology, it is very important for researchers to use standardized methods for an effective analysis of the results, preventing variability due to methodology.