Enterocytozoon hepatopenaei (EHP) was first described in Thailand in 2009 and has since been identified as a significant threat to the shrimp aquaculture industry. Recently, intracellular microsporidia were identified as a causative agent of hepatopancreatic microsporidiosis (HPM). To date, HPM has been listed as an emerging threat to shrimp farming industries because of reduced shrimp growth and survival rates which are considered to be a wasting disease. This study investigated the outbreaks of HPM in farmed Penaeus vannamei in Taiwan. Sixty-five shrimp samples were collected from Taiwan. The proportion of HPM-positive cases was 48% (31/65). Additionally, the gross signs in infected shrimp were stunted growth, sloughed hepatopancreas (HP), and lethargy. The smear impression on the HP also revealed the existence of large EHP spores. Nested-PCR findings identified that 9 cases were confirmed to be positive for the EhSWP1 gene in the first step and 22 cases tested positive for the second step. Phylogenetic analysis of EHP from Taiwan showed 100% similarity to EHP from Thailand, India, and the United States. Histopathological analysis of the HP revealed haemocyte infiltration and the presence of EHP spores in the hepatopancreatic tubule epithelial cells. These results demonstrated that EHP is the main cause in shrimp farms in Taiwan.