The black gill disease of Litopenaeus vannamei is a major problem of shrimp farmers culturing in brackish marine and fresh water in India. The normal and black gill infected shrimps were collected from shrimp grow-out ponds situated in the banks of Vellar Estuary. The infected shrimp gills were collected from both normal and infected shrimps. The HNE (Hematoxylin and eosin) staining based histopathological study of infected gills confirmed the fungal infection in the black gill lamellae of the infected shrimp. Further the same gill samples were subjected to microbiological analysis for fungal culture in PDA (Potato Dextrose Agar). The cultured fungi showed white color mycelium with brown colored spores. Under the light microscope, the fungi look like Ascomycota. Further, the fungal strain was confirmed by molecular analysis. The fungal DNA was isolated, amplified with Universal ITS primer confirmed that the species was Aspergillus terreus.