A total of 291 white leg shrimp samples were collected from 70 cultured ponds in Soc Trang, Bac Lieu and Ca Mau provinces in the Mekong Delta and subjected to endoparasitic detection in the digestive tract. Collected shrimps displayed unhealthy behaviors such as stop or less feeding and lethagic swimming. Pathological signs in the gastrointestinal tract include (1) empty midgut and stomach together with pale and atrophy hepatopancreas; (2) empty, little or discontinued food in the midgut; (3) slow growth and variation in sizes; and (4) white feces. The results from fresh and Giemsa stained smears methods revealed that 96.5% of sampled shrimps were infected by gregarine parasite at different developmental stages. A prevalence infection of 24.7% was recorded with Vermiform present in the hepatopancreas by fresh smear and histology. Histopathological analysis noted that 7.9% of collected shrimp samples had Enterocytozoon hepatopenaei (EHP) spores in hepatopancreas and midgut and confirmed by PCR analysis.