In response to the constant challenge by potential pathogens, external surfaces of fish, their skin, gills and intestinal tract, are coated with mucus, a gel like substance which largely prevents the entry of pathogens. This mucus gel consists mainly of water and mucins, large O-glycosylated proteins, which are responsible for forming a gel like mixture. A modulation of the mRNA expression of mucins, was described in viral diseases in mammals however there is a knowledge gap about the regulation of mucins during viral infection in fish. Therefore, novel sequences for common carp mucins were located in an early version of the common carp genome and their mRNA expression measured in carp under infection with three different viral pathogens: (i) the alloherpesvirus cyprinid herpesvirus 3, (ii) the rhabdovirus spring viremia of carp virus and (iii) the poxvirus carp edema virus. The results showed a downregulation of mucin mRNA expression in gills and gut of common carp under infection with these pathogenic viruses. This could be a sign of a severe distress to the mucosal tissues in carp which occurs under viral infection. The reduced expression of mucins could help explaining the increased susceptibility of virus-infected carp to secondary bacterial infection.