Slow growth of farmed has been reported throughout shrimp growing areas of Zhoushan since 2013, resulting in severe economic losses for high density farmers. Bacterial culture, histopathology, and polymerase chain reaction analyses were conducted to identify the pathogenicity of these slow growing, multiple infections. Infectious hypodermal and hematopoietic necrosis virus (IHHNV) and the microsporidian (EHP), which are typical slow-growing pathogens, were analyzed by polymerase chain reaction in 270 samples collected from high-density, slow-growing Zhoushan shrimp in farm ponds. The results showed a high incidence of EHP (230/270, 85.19%), but no evidence of IHHNV infection. Bacteria were not consistently isolated from the diseased shrimp, and EHP and IHHNV were not detected in any normal appearing shrimp. A BLAST analysis of the sequenced product revealed 99.55% similarity with the matching region of small subunit rRNA from EHP (KF362130). Histopathological sections showed microsporidial spores only in the cytoplasm of hepatopancreatic tubule epithelial cells from diseased shrimp. Based on the ultrastructural features of the family and the cytoplasmic location of the plasmodia, the pathogen causing slow growth syndrome in Zhoushan was EHP. EHP is a microsporidian parasite that was first isolated and characterized from the giant or black tiger shrimp . Although EHP does not appear to cause mortality, shrimp farmers have reported that it is associated with severely retarded growth in compared with their unaffected counterparts. No specific signs were observed in shrimp at the early stage of pathogenicity, which differs from the most common microsporidian reported previously from cotton shrimp. Further studies are required to understand the interaction between this host and pathogen.