Indian white shrimp (Penaeus indicus) which is an endemic species of India was found to be infected with Black gill disease. P.indicus collected from wild had black coloured gill which is a typical sign of black gill disease. Morphological examination of the developed culture isolated from the gill of shrimp showed similarity to Rhizopus sp., molecular phylogenetic analysis was done for species confirmation, histopathological observation of the infected gill showed inflammatory responses of P.indicus against Rhizopus sp., which cause haemocytic infiltration, encapsulation, melanization and collagen-like fibre deposition and the spore isolated was studied under scanning electron microscope (SEM).