Recently, The shrimp cultured in these farms such as Taiwan, Tailand and other Southeast Asia were severely infected with Enterocytozoon hepatopenaei (EHP), which is a microsporidian parasite that infects the hepatopancreas of slow-growing Penaeus monodon and Penaeus vannamei, becoming more and more common and the economic losses are now considered to critically affect the shrimp aquaculture directly or indirectly. Farm samples in the experiment used of shrimps in a total of 29 individuals collected from farms at Yilan, Tainan, and Kaohsiung city in Taiwan. The detection of EHP by recombinase polymerase amplification is recognized the better standard for detecting in shrimp pathogens due to their sensitivity, specificity, and rapidity than other methods for the detection of EHP be carried out by molecular assay (PCR, qPCR, histology). The aim of this study was to establish a rapid detection method with high sensitivity and high specificity not only can help to detect EHP more accurately but also can be used for detection in farm samples.