In this study, we described the partial structure, mRNA tissue distribution and regulation of two carp mucin and two β-defensin genes. This is the first description of these genes in fish. The genes might provide relevant tools to monitor feed-related improvements of fish health under aquaculture conditions. Carp mucin 2 and mucin 5B genes show a high similarity to their mammalian and avian counterparts. The carp β-defensin 1 and β-defensin 2 genes cluster together well with their piscine family members. The influence of a β-glucan immunomodulant on the expression of these genes in mucosal tissues could be confirmed for the first time. Muc5B expression was significantly increased in the skin. For Muc2 no significant up- or down-regulation could be observed. Significantly higher expression levels of β-defensin 2 in gills and both β-defensin genes in skin were found. Thus, the mucosal system can be influenced by the addition of β-glucans to the food.