Isopods are parasitic crustaceans that pose serious threat to fisheries. Several studies have tried to explore the host-pathogen relationship between marine fishes and isopods. The present study aims to understanding the secondary infections in marine fishes pertaining to isopods. To assess the secondary infection in infected fishes, parasite infested and healthy tissues of fishes were collected. The samples were subjected to standard microbiological procedure to identify the presence of pathogenic bacteria and fungi. Our results showed the branchial region had the higher microbial load of non-sporulating cenocytic fungi in infected fishes. Moreover, fungal strains isolated from the parasitic lesion confirmed that the parasitation and body lesion facilitates the entry of several pathogenic microbes at the damaged host tissue. More over the immune regulation of fish fights back by producing minute cysts, trying to encapsulate the growing fungus. But this may eventually lead to systemic infestation and death of the fish.