ABSTRACT: The microsporidian parasite, Enterocytozoon hepatopenaei (EHP), is an emerging problem in the marine shrimp industry, primarily in Asian countries such as China, Thailand, India, Malaysia, Indonesia, and Vietnam. A screening for EHP was conducted to investigate the prevalence of EHP after a fixed period of culturing for 1 rearing cycle to study the prevalence of EHP infection in 3 states of Malaysia. The screening stages covered Penaeus vannamei postlarvae (PL), 14–30, 31–50, 51–70, and 71–90 d of culture in 1 production cycle. A total of 279 samples were amplified using a PCR assay targeting the gene encoding a spore wall protein (SWP) of EHP (SWP-PCR). The EHP infection was initially detected in the hatchery and increased to 96.6% after the shrimp were transferred to the pond. The positive EHP sequence showed 91–100% similarity to sequences from India, Thailand, Vietnam, Indonesia, and Latin America. The infection of EHP increased throughout 1 rearing cycle due to certain factors such as the cannibalistic feeding habits of shrimp and the presence of unknown vectors or carriers of EHP in the culture ponds. Hence, the finding from the current study will be fundamental for other studies such as potential vector and control measure.