The innate immune system of fish is considered first line of defense against a broad spectrum of pathogens. Being a component of innate immunity and lying at the interface between fish and the aqueous environment, skin mucus plays a frontier role in protecting fish from infections. In the present study, skin mucus of Cirrhinus mrigala, Labeo rohita, Catla catla, Rita rita and Channa punctata, inhabiting different ecological niches, was analyzed to characterize potential innate immune factors such as lysozyme, proteases, phosphatases, esterase and sialic acid. The enzyme activities were high in bottom dweller species, C. punctata and C. mrigala, and low in clean water inhabiting species, L. rohita and C. catla. An inverse relationship was observed between the level of enzyme activity and the sialic acid content in these fish species. In R. rita, however, the levels of all factors were found to be low. Zymographic analysis with labeled Micrococcus lysodeikticus revealed three isoforms of lysozyme in C. punctata and two in each species, C. mrigala, L. rohita and C. catla. In R. rita, lysozyme could not be detected. Gelatin zymography revealed that serine and metalloproteases were the major mucus proteases in all fish species investigated. In addition, trypsin-like protease and Ca(++)-specific serine proteases were observed in skin mucus. Increased knowledge of these parameters could be useful in understanding the role of skin mucus in the innate immune system of fish species inhabiting different ecological niches.